Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000969.1 Kokia drynarioides strain JFW-HI SEQ_112149, 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: 79629
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:22 original size:4 final size:4
Alignment explanation
Indices: 13--44 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
3 CCTCTCCTTC
13 TTCT TTCT TTCT TTCT TTCCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTC
45 CCGTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:37 original size:13 final size:13
Alignment explanation
Indices: 13--45 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3 CCTCTCCTTC
13 TTCTTT-CTTTCT
1 TTCTTTCCTTTCT
25 TTCTTTCCTTTCT
1 TTCTTTCCTTTCT
38 TTCTTTCC
1 TTCTTTCC
46 CGTTTATTTG
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:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTCTTTCCTTTCT
Found at i:2719 original size:30 final size:30
Alignment explanation
Indices: 2685--2896 Score: 201
Period size: 30 Copynumber: 7.3 Consensus size: 30
2675 TAAAATTGTT
*
2685 TTTGACCCCTAAATTTTCTAAAAA-TCTAAA
1 TTTGACCCCTAAATTTTCCAAAAATTC-AAA
*
2715 TTTGA--CTTAAATTTTCCAAAAATTCAAA
1 TTTGACCCCTAAATTTTCCAAAAATTCAAA
* *
2743 TTTAACCCCTAACTTTT-CAAAAATTCAAA
1 TTTGACCCCTAAATTTTCCAAAAATTCAAA
* *
2772 TTTGACCCCTAAATTTTCCAAATATTTAAA
1 TTTGACCCCTAAATTTTCCAAAAATTCAAA
*
2802 TTTGA-CCCTCAAATTTTCCAAAAATTCCAA
1 TTTGACCCCT-AAATTTTCCAAAAATTCAAA
* * * *
2832 TTT-AACCCTAAACTTTT--TAAAA-TCCAG
1 TTTGACCCCTAAA-TTTTCCAAAAATTCAAA
*
2859 TTTAACCCCTAAAGTTTT-CAAAAATTCAAA
1 TTTGACCCCTAAA-TTTTCCAAAAATTCAAA
*
2889 TTTAACCC
1 TTTGACCC
2897 GATTTTAATT
Statistics
Matches: 153, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
27 7 0.05
28 38 0.25
29 41 0.27
30 67 0.44
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (30 bp):
TTTGACCCCTAAATTTTCCAAAAATTCAAA
Found at i:2786 original size:87 final size:84
Alignment explanation
Indices: 2685--2891 Score: 247
Period size: 87 Copynumber: 2.4 Consensus size: 84
2675 TAAAATTGTT
*
2685 TTTGACCCCTAAATTTTCTAAAAATCTAAATTTGA-CTTAAATTTTCCAAAAATTCAAATTTAAC
1 TTTGACCCCTAAATTTTC-AAAAAT-TAAATTTGACCTCAAATTTTCCAAAAATTCAAATTTAA-
2749 CCCT-AACTTTTCAAAAATTCAAA
63 CCCTAAACTTTT-AAAAA-TCAAA
* *
2772 TTTGACCCCTAAATTTTCCAAATATTTAAATTTGACCCTCAAATTTTCCAAAAATTCCAATTTAA
1 TTTGACCCCTAAATTTT-CAAA-AATTAAATTTGA-CCTCAAATTTTCCAAAAATTCAAATTTAA
* * *
2837 CCCTAAACTTTTTAAAATCCAG
63 CCCTAAACTTTTAAAAATCAAA
*
2859 TTTAACCCCTAAAGTTTTCAAAAATTCAAATTT
1 TTTGACCCCTAAA-TTTTCAAAAATT-AAATTT
2892 AACCCGATTT
Statistics
Matches: 105, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
86 3 0.03
87 54 0.51
88 15 0.14
89 33 0.31
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (84 bp):
TTTGACCCCTAAATTTTCAAAAATTAAATTTGACCTCAAATTTTCCAAAAATTCAAATTTAACCC
TAAACTTTTAAAAATCAAA
Found at i:4975 original size:31 final size:31
Alignment explanation
Indices: 4940--5007 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
4930 TGCATATGCA
4940 TTCATGCATTCATAAAATTCCGCATCACATT
1 TTCATGCATTCATAAAATTCCGCATCACATT
* ** *
4971 TTCATGCATTCATAAAGTTTTGCATCGCATT
1 TTCATGCATTCATAAAATTCCGCATCACATT
5002 TTCATG
1 TTCATG
5008 TATTAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (31 bp):
TTCATGCATTCATAAAATTCCGCATCACATT
Found at i:13164 original size:50 final size:50
Alignment explanation
Indices: 13110--13214 Score: 156
Period size: 50 Copynumber: 2.1 Consensus size: 50
13100 AGGTGCAAAT
*
13110 TGAAGCAGCAATGGCAAATCTCATACACCTAAAACTGTAGAGAGGTAGAA
1 TGAAGCAGCAATGGCAAATCACATACACCTAAAACTGTAGAGAGGTAGAA
* * * * *
13160 TGAAGCCGCAATGGCAAATCACATTCACCTAAAGCTGTAGAGGGGTAGAT
1 TGAAGCAGCAATGGCAAATCACATACACCTAAAACTGTAGAGAGGTAGAA
13210 TGAAG
1 TGAAG
13215 TCACAAGGAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (50 bp):
TGAAGCAGCAATGGCAAATCACATACACCTAAAACTGTAGAGAGGTAGAA
Found at i:13465 original size:91 final size:92
Alignment explanation
Indices: 13351--13563 Score: 324
Period size: 91 Copynumber: 2.3 Consensus size: 92
13341 AAGTAATCTA
* * * *
13351 GATCTCTTACCCCTAAGTTAAGAGGGGCAGATTG-AAGATCGTTACAATCTTTTACCCTTAAATC
1 GATCTCTTACCCCTAAGTCAAGAGGGGCAGATTGAAAGACCATTACAATCTTTTACCCCTAAATC
*
13415 AAGAGGGGCTGATTGAAGCCACATTCC
66 AAGAGGGGCAGATTGAAGCCACATTCC
* *
13442 GATCTCTTACCCCTAAGTCAAGAGGGGCA-AATGAAAGACCATTCCAATCTTTTACCCCTAAATC
1 GATCTCTTACCCCTAAGTCAAGAGGGGCAGATTGAAAGACCATTACAATCTTTTACCCCTAAATC
13506 AAGAGGGGCAGATTGAAGCCACATTCC
66 AAGAGGGGCAGATTGAAGCCACATTCC
* *
13533 GATCTTTTACCCCTAA-TCGAGAGGGGCAGAT
1 GATCTCTTACCCCTAAGTCAAGAGGGGCAGAT
13564 CAAACGTCCA
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
90 14 0.13
91 96 0.87
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (92 bp):
GATCTCTTACCCCTAAGTCAAGAGGGGCAGATTGAAAGACCATTACAATCTTTTACCCCTAAATC
AAGAGGGGCAGATTGAAGCCACATTCC
Found at i:13468 original size:46 final size:46
Alignment explanation
Indices: 13351--13563 Score: 247
Period size: 45 Copynumber: 4.7 Consensus size: 46
13341 AAGTAATCTA
* * * * *
13351 GATCTCTTACCCCTAAGTTAAGAGGGGCAGATTGAAG--ATCGTTAC
1 GATCTTTTACCCCTAAATCAAGAGGGGCAGATTGAAGCCA-CATTCC
* * *
13396 AATCTTTTACCCTTAAATCAAGAGGGGCTGATTGAAGCCACATTCC
1 GATCTTTTACCCCTAAATCAAGAGGGGCAGATTGAAGCCACATTCC
* * * *
13442 GATCTCTTACCCCTAAGTCAAGAGGGGCA-AATGAAAGAC-CATTCC
1 GATCTTTTACCCCTAAATCAAGAGGGGCAGATTG-AAGCCACATTCC
*
13487 AATCTTTTACCCCTAAATCAAGAGGGGCAGATTGAAGCCACATTCC
1 GATCTTTTACCCCTAAATCAAGAGGGGCAGATTGAAGCCACATTCC
*
13533 GATCTTTTACCCCT-AATCGAGAGGGGCAGAT
1 GATCTTTTACCCCTAAATCAAGAGGGGCAGAT
13564 CAAACGTCCA
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
45 86 0.61
46 54 0.38
47 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (46 bp):
GATCTTTTACCCCTAAATCAAGAGGGGCAGATTGAAGCCACATTCC
Found at i:15050 original size:89 final size:88
Alignment explanation
Indices: 14924--15164 Score: 290
Period size: 90 Copynumber: 2.7 Consensus size: 88
14914 AAAATTATTT
* * *
14924 TTTGACCCCTAAATTTTCCAAAAATCTGAATTTAACCCTTAAATTTTCTAAAATTCAAATTTAA-
1 TTTGACCCCTAAACTTTCTAAAAATTTGAATTTAACCC-TAAATTTTCTAAAATTCAAATTTAAC
* * **
14988 CCTCTAAACTTTCTAAAAATTTGAA
65 CCT-TAAAATTTCCAAAAATTCCAA
*
15013 TTTGACCCCTAAACTTTCTAAAAATTTGAATTTAACCCCTAAATTTTCTAAAAATT-ACAATTTG
1 TTTGACCCCTAAACTTTCTAAAAATTTGAATTTAA-CCCTAAATTTTCT-AAAATTCA-AATTTA
15077 ACCCTTAAAATTTCCAAAAATTCCAA
63 ACCCTTAAAATTTCCAAAAATTCCAA
* * * *
15103 TTTGACCCTTAAACTTTCTAAAATTTTTGAA-TTGACCCTACAATTTTCAAAAATTCAAATTT
1 TTTGACCCCTAAACTTTCTAAAA-ATTTGAATTTAACCCTA-AATTTTCTAAAATTCAAATTT
15165 GACTCGATTT
Statistics
Matches: 133, Mismatches: 12, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
89 59 0.44
90 65 0.49
91 9 0.07
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (88 bp):
TTTGACCCCTAAACTTTCTAAAAATTTGAATTTAACCCTAAATTTTCTAAAATTCAAATTTAACC
CTTAAAATTTCCAAAAATTCCAA
Found at i:15061 original size:60 final size:60
Alignment explanation
Indices: 14928--15164 Score: 257
Period size: 60 Copynumber: 4.0 Consensus size: 60
14918 TTATTTTTTG
* * * * *
14928 ACCCCTAAATTTTCCAAAAATCTGAATTTAACCCTTAAATTTTCT-AAAATTCAAATTTA
1 ACCCCTAAACTTTCTAAAAATTTGAATTTGACCCCTAAATTTTCTAAAAATTCAAATTTA
* * **
14987 ACCTCTAAACTTTCTAAAAATTTGAATTTGACCCCTAAACTTTCTAAAAATTTGAATTTA
1 ACCCCTAAACTTTCTAAAAATTTGAATTTGACCCCTAAATTTTCTAAAAATTCAAATTTA
* ** * * * * *
15047 ACCCCTAAATTTTCTAAAAATTACAATTTGACCCTTAAAATTTCCAAAAATTCCAATTTG
1 ACCCCTAAACTTTCTAAAAATTTGAATTTGACCCCTAAATTTTCTAAAAATTCAAATTTA
* *
15107 ACCCTTAAACTTTCTAAAATTTTTGAA-TTGA-CCCTACAATTTTC-AAAAATTCAAATTT
1 ACCCCTAAACTTTCTAAAA-ATTTGAATTTGACCCCTA-AATTTTCTAAAAATTCAAATTT
15165 GACTCGATTT
Statistics
Matches: 148, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
59 55 0.37
60 89 0.60
61 4 0.03
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (60 bp):
ACCCCTAAACTTTCTAAAAATTTGAATTTGACCCCTAAATTTTCTAAAAATTCAAATTTA
Found at i:15138 original size:30 final size:30
Alignment explanation
Indices: 14924--15167 Score: 219
Period size: 30 Copynumber: 8.2 Consensus size: 30
14914 AAAATTATTT
* * * *
14924 TTTGACCCCTAAATTTTCCAAAAATCTGAA
1 TTTGACCCTTAAACTTTCTAAAAATTTGAA
* * **
14954 TTTAACCCTTAAATTTTCT-AAAATTCAAA
1 TTTGACCCTTAAACTTTCTAAAAATTTGAA
*
14983 TTT-AACCTCTAAACTTTCTAAAAATTTGAA
1 TTTGACCCT-TAAACTTTCTAAAAATTTGAA
*
15013 TTTGACCCCTAAACTTTCTAAAAATTTGAA
1 TTTGACCCTTAAACTTTCTAAAAATTTGAA
* * * **
15043 TTTAACCCCTAAATTTTCTAAAAATTACAA
1 TTTGACCCTTAAACTTTCTAAAAATTTGAA
* * **
15073 TTTGACCCTTAAAATTTCCAAAAATTCCAA
1 TTTGACCCTTAAACTTTCTAAAAATTTGAA
*
15103 TTTGACCCTTAAACTTTCTAAAATTTTTGAA
1 TTTGACCCTTAAACTTTCTAAAA-ATTTGAA
* **
15134 -TTGACCC-TACAATTTTC-AAAAATTCAAA
1 TTTGACCCTTA-AACTTTCTAAAAATTTGAA
15162 TTTGAC
1 TTTGAC
15168 TCGATTTTAA
Statistics
Matches: 178, Mismatches: 30, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
28 8 0.04
29 30 0.17
30 133 0.75
31 7 0.04
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (30 bp):
TTTGACCCTTAAACTTTCTAAAAATTTGAA
Found at i:16267 original size:15 final size:14
Alignment explanation
Indices: 16244--16282 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
16234 GAATATATAT
16244 AATTCAAAAAATAAA
1 AATT-AAAAAATAAA
* *
16259 AATTAAAAAGTTAA
1 AATTAAAAAATAAA
16273 AATTAAAAAA
1 AATTAAAAAA
16283 AAGCTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (14 bp):
AATTAAAAAATAAA
Found at i:16658 original size:27 final size:29
Alignment explanation
Indices: 16628--16682 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
16618 CAAATTTTTT
* *
16628 ATTTTT-ACTTTTTTTAA-TTATATATTA
1 ATTTTTGAATTTTTATAATTTATATATTA
16655 ATTTTTGAATTTTTATAATTTATATATT
1 ATTTTTGAATTTTTATAATTTATATATT
16683 TTTCTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 9 0.38
29 9 0.38
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
ATTTTTGAATTTTTATAATTTATATATTA
Found at i:22376 original size:75 final size:75
Alignment explanation
Indices: 22253--22683 Score: 494
Period size: 75 Copynumber: 5.8 Consensus size: 75
22243 TATTAAGTTT
* * * * * *
22253 TTGCACCCAGCACTAGTC-AGATAACCGACAAATATAAGAAATGTGCCCAGCACTAGTAAGATAA
1 TTGCGCCCAGCGCTAGTCGA-ATAACCGACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAA
22317 ACT-AGCAAAGG
65 ACTGA-CAAAGG
* * * **
22328 TTGCACCCAGCGCTAGTCGAATAACCAATGAATATAAGAAGTGTGCCCAGTACTAGTCAGATAAA
1 TTGCGCCCAGCGCTAGTCGAATAACCGACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAAA
22393 CTGACAAAGG
66 CTGACAAAGG
* * * * *
22403 TTGCGCCCAGCGCTAGTTGGATAATCGACGAATATAAGAAGTGTGCCCAACACCAGTCAAATAAA
1 TTGCGCCCAGCGCTAGTCGAATAACCGACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAAA
*
22468 CTGAAAAAGG
66 CTGACAAAGG
* * * * * *
22478 TTGCGTCCAACACTAGTCGGATAACCAACGAATAGAAGAAGTGTGCCCAACACTAGTCAGATAAA
1 TTGCGCCCAGCGCTAGTCGAATAACCGACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAAA
*
22543 TTGACAAAGG
66 CTGACAAAGG
* * *
22553 TTACGCCCAGCGCTAGTCGAATAATCGACGAATATAAGAAGTGTGCCTAACACTAGTCAGATAAA
1 TTGCGCCCAGCGCTAGTCGAATAACCGACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAAA
*
22618 CTAACAAAGG
66 CTGACAAAGG
* * * * *
22628 TTGCGCCCAGCGTTAGTC-AGATAATCGACG-ATACTAA-ATGTGAGCCCAACTCTAGT
1 TTGCGCCCAGCGCTAGTCGA-ATAACCGACGAATA-TAAGAAGTGTGCCCAACACTAGT
22684 TGGATATACC
Statistics
Matches: 306, Mismatches: 46, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
74 19 0.06
75 285 0.93
76 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (75 bp):
TTGCGCCCAGCGCTAGTCGAATAACCGACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAAA
CTGACAAAGG
Found at i:22419 original size:35 final size:35
Alignment explanation
Indices: 22297--22651 Score: 82
Period size: 35 Copynumber: 9.6 Consensus size: 35
22287 TAAGAAATGT
*
22297 GCCCAGCACTAGTAAGATAAACT-AGCAAAGGTTGC
1 GCCCAGCACTAGTCAGATAAACTGA-CAAAGGTTGC
* * * * *
22332 ACCCAGCGCTAGTC-GAATAACCAATGAATATAAGAAG-TGT
1 GCCCAGCACTAGTCAG-ATAA--ACTG-ACA-AAG--GTTGC
*
22372 GCCCAGTACTAGTCAGATAAACTGACAAAGGTTGC
1 GCCCAGCACTAGTCAGATAAACTGACAAAGGTTGC
* ** * *
22407 GCCCAGCGCTAGTTGGATAATCGAC-GAATATAAGAAG-TGT
1 GCCCAGCACTAGTCAGATAA---ACTG-ACA-AAG--GTTGC
* * * *
22447 GCCCAACACCAGTCAAATAAACTGAAAAAGGTTGC
1 GCCCAGCACTAGTCAGATAAACTGACAAAGGTTGC
* * * * *
22482 GTCCAACACTAGTCGGATAACCAAC-GAATAGAAGAAG-TGT
1 GCCCAGCACTAGTCAGAT-A--AACTG-ACA-AAG--GTTGC
* * *
22522 GCCCAACACTAGTCAGATAAATTGACAAAGGTTAC
1 GCCCAGCACTAGTCAGATAAACTGACAAAGGTTGC
* * *
22557 GCCCAGCGCTAGTC-GAATAATCGAC-GAATATAAGAAG-TGT
1 GCCCAGCACTAGTCAG-ATAA---ACTG-ACA-AAG--GTTGC
* * *
22597 GCCTAACACTAGTCAGATAAACTAACAAAGGTTGC
1 GCCCAGCACTAGTCAGATAAACTGACAAAGGTTGC
**
22632 GCCCAGCGTTAGTCAGATAA
1 GCCCAGCACTAGTCAGATAA
22652 TCGACGATAC
Statistics
Matches: 227, Mismatches: 54, Indels: 78
0.63 0.15 0.22
Matches are distributed among these distances:
34 6 0.03
35 84 0.37
36 13 0.06
37 19 0.08
38 18 0.08
39 14 0.06
40 67 0.30
41 6 0.03
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (35 bp):
GCCCAGCACTAGTCAGATAAACTGACAAAGGTTGC
Found at i:24104 original size:16 final size:16
Alignment explanation
Indices: 24085--24116 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24075 CCTTTTTATT
24085 TTTTTACTTTAATTTA
1 TTTTTACTTTAATTTA
*
24101 TTTTTATTTTAATTTA
1 TTTTTACTTTAATTTA
24117 ACCCTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTACTTTAATTTA
Found at i:24254 original size:28 final size:27
Alignment explanation
Indices: 24223--24282 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
24213 CCTTTTATTT
*
24223 ATTTTTAAAAAAAAATTAAACCCTTTTA
1 ATTTTT-AAAAAAAATTAAACCCTTTCA
* *
24251 ATTTTTAAAAAAAATTTAATCCTTTCA
1 ATTTTTAAAAAAAATTAAACCCTTTCA
24278 ATTTT
1 ATTTT
24283 ATTTCTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (27 bp):
ATTTTTAAAAAAAATTAAACCCTTTCA
Found at i:24481 original size:20 final size:20
Alignment explanation
Indices: 24444--24482 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
24434 ATCTAGTTTG
*
24444 TTTTATCTATGATTATTTTA
1 TTTTATCTATCATTATTTTA
*
24464 TTTTA-CTATCATTAATTTA
1 TTTTATCTATCATTATTTTA
24483 AATTGTATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATCTATCATTATTTTA
Found at i:25968 original size:51 final size:51
Alignment explanation
Indices: 25734--25961 Score: 323
Period size: 51 Copynumber: 4.4 Consensus size: 51
25724 TTTCGTTTAA
** * *
25734 TACTCACGATGACA-TATAGTCATCAGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCAGACCT-TTAATCCATAAAGG-ATTCATT
* * * *
25787 CACTCACGATGACACTGAGTCATCAGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCATAAAGGATTCATT
*
25838 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCATAAAGGATTCATT
* *
25889 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCATAAAGGATTCATT
25940 TACTCACGATGACACTTAGTCA
1 TACTCACGATGACACTTAGTCA
25962 CCGGACCCTT
Statistics
Matches: 160, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
51 124 0.77
52 9 0.06
53 26 0.16
54 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCAGACCTTTAATCCATAAAGGATTCATT
Found at i:30591 original size:105 final size:105
Alignment explanation
Indices: 30462--30678 Score: 409
Period size: 105 Copynumber: 2.1 Consensus size: 105
30452 CGTTGGAGGG
*
30462 TAAA-TGGAAATGCAATGGAGGAGGAAAAAAGGAGAATTTCGATAGAGGTGGAGAACAAATGGGA
1 TAAATTGGAAATGCAATGGAGGAGGAAAAAAGGAGAATTTCAATAGAGGTGGAGAACAAATGGGA
*
30526 GAGGAGAAGACAAAACAAGGAAAAAGGTTTAAAAACTCAA
66 GAGGAGAAAACAAAACAAGGAAAAAGGTTTAAAAACTCAA
30566 TAAATTGGAAATGCAATGGAGGAGGAAAAAAGGAGAATTTCAATAGAGGTGGAGAACAAATGGGA
1 TAAATTGGAAATGCAATGGAGGAGGAAAAAAGGAGAATTTCAATAGAGGTGGAGAACAAATGGGA
30631 GAGGAGAAAACAAAACAAGGAAAAAGGTTTAAAAACTCAA
66 GAGGAGAAAACAAAACAAGGAAAAAGGTTTAAAAACTCAA
30671 TAAATTGG
1 TAAATTGG
30679 GTAATTTACA
Statistics
Matches: 110, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
104 4 0.04
105 106 0.96
ACGTcount: A:0.50, C:0.06, G:0.29, T:0.15
Consensus pattern (105 bp):
TAAATTGGAAATGCAATGGAGGAGGAAAAAAGGAGAATTTCAATAGAGGTGGAGAACAAATGGGA
GAGGAGAAAACAAAACAAGGAAAAAGGTTTAAAAACTCAA
Found at i:39950 original size:37 final size:37
Alignment explanation
Indices: 39903--39977 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
39893 CTATTGGAAG
39903 TATATATGTTTTGTATACAGATAATTCTTGAGAAATA
1 TATATATGTTTTGTATACAGATAATTCTTGAGAAATA
39940 TATATATGTTTTGTATACAGATAATTCTTGAGAAATA
1 TATATATGTTTTGTATACAGATAATTCTTGAGAAATA
39977 T
1 T
39978 CAAAGTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.44
Consensus pattern (37 bp):
TATATATGTTTTGTATACAGATAATTCTTGAGAAATA
Found at i:46224 original size:86 final size:86
Alignment explanation
Indices: 46079--46251 Score: 328
Period size: 86 Copynumber: 2.0 Consensus size: 86
46069 GTTCAATTTG
* *
46079 TAAGAATCAAAAAATACTCAAACCTATCTCACCTTCCTCTATCACTAAAAATATATCAATCAATT
1 TAAGAATCAAAAAATACTCAAACCCATCTCACCTTCCTCTATCACTAAAAATACATCAATCAATT
46144 ATATAAAACTTTTGTTTTCTT
66 ATATAAAACTTTTGTTTTCTT
46165 TAAGAATCAAAAAATACTCAAACCCATCTCACCTTCCTCTATCACTAAAAATACATCAATCAATT
1 TAAGAATCAAAAAATACTCAAACCCATCTCACCTTCCTCTATCACTAAAAATACATCAATCAATT
46230 ATATAAAACTTTTGTTTTCTT
66 ATATAAAACTTTTGTTTTCTT
46251 T
1 T
46252 CTTTCTTTCT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.35
Consensus pattern (86 bp):
TAAGAATCAAAAAATACTCAAACCCATCTCACCTTCCTCTATCACTAAAAATACATCAATCAATT
ATATAAAACTTTTGTTTTCTT
Found at i:46254 original size:4 final size:4
Alignment explanation
Indices: 46245--46271 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
46235 AAACTTTTGT
46245 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
46272 TCATTGACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:63160 original size:2 final size:2
Alignment explanation
Indices: 63155--63183 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
63145 TTTCATATGG
63155 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
63184 TTCCAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:64850 original size:33 final size:33
Alignment explanation
Indices: 64772--64851 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
64762 TTGGGAGGGT
* *
64772 TTGGGCAAAAATCATTAGGCCTGAAAAATGGGC
1 TTGGGCAAAAATTATTAAGCCTGAAAAATGGGC
* * *
64805 TTGGGCAGAAATTATTAAGTCTGAAACAT-GGC
1 TTGGGCAAAAATTATTAAGCCTGAAAAATGGGC
64837 TTGGGCCAAAAATTA
1 TTGGG-CAAAAATTA
64852 GGCCCAAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 8 0.20
33 32 0.80
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (33 bp):
TTGGGCAAAAATTATTAAGCCTGAAAAATGGGC
Found at i:65463 original size:15 final size:15
Alignment explanation
Indices: 65443--65474 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
65433 ATAATATCAG
65443 CACTTTCTCCTTCAA
1 CACTTTCTCCTTCAA
65458 CACTTTCTCCTTCAA
1 CACTTTCTCCTTCAA
65473 CA
1 CA
65475 AAATAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.38
Consensus pattern (15 bp):
CACTTTCTCCTTCAA
Found at i:73826 original size:18 final size:19
Alignment explanation
Indices: 73803--73838 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
73793 AACTTTCCAT
73803 TTTA-TTATTTTTTCTTTA
1 TTTATTTATTTTTTCTTTA
73821 TTTATTTATTTTTTCTTT
1 TTTATTTATTTTTTCTTT
73839 TCATATTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTATTTATTTTTTCTTTA
Found at i:73884 original size:17 final size:18
Alignment explanation
Indices: 73807--73885 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
73797 TTCCATTTTA
73807 TTATTTT-TTC-TTTA-T
1 TTATTTTATTCTTTTATT
*
73822 TTA-TTTATT-TTTTCTT
1 TTATTTTATTCTTTTATT
* *
73838 TTCATATTGTCTTTTTTTATT
1 TT-AT-TT-TATTCTTTTATT
73859 TTATTTTATTCTTTTATT
1 TTATTTTATTCTTTTATT
73877 TT-TTTTATT
1 TTATTTTATT
73886 TTCAATTGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 3 0.06
15 8 0.16
16 3 0.06
17 8 0.16
18 12 0.24
19 4 0.08
20 5 0.10
21 8 0.16
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (18 bp):
TTATTTTATTCTTTTATT
Found at i:73885 original size:22 final size:21
Alignment explanation
Indices: 73847--73887 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
73837 TTTCATATTG
73847 TCTTTTTTTATTTTATTTTAT
1 TCTTTTTTTATTTTATTTTAT
*
73868 TCTTTTATTTTTTTTATTTT
1 TCTTTT-TTTATTTTATTTT
73888 CAATTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (21 bp):
TCTTTTTTTATTTTATTTTAT
Found at i:75174 original size:25 final size:23
Alignment explanation
Indices: 75146--75191 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
75136 GTTGGATCCT
75146 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATT-TAAAAA-ATAATTTG
*
75171 AATTAAATTTAAACAATAATT
1 AATTAAATTTAAAAAATAATT
75192 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTTG
Found at i:75199 original size:25 final size:26
Alignment explanation
Indices: 75144--75199 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
75134 TAGTTGGATC
75144 CTAATTAAATTCTAAAAAGATAATTT
1 CTAATTAAATTCTAAAAAGATAATTT
* *
75170 -GAATTAAATT-TAAACA-ATAATTCT
1 CTAATTAAATTCTAAAAAGATAATT-T
75194 CTAATT
1 CTAATT
75200 GGATCCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 6 0.24
24 6 0.24
25 13 0.52
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (26 bp):
CTAATTAAATTCTAAAAAGATAATTT
Found at i:76232 original size:13 final size:12
Alignment explanation
Indices: 76214--76289 Score: 50
Period size: 13 Copynumber: 6.2 Consensus size: 12
76204 CACTTTTGTC
76214 TTTTTCTCTTTCT
1 TTTTTCTCTTT-T
***
76227 TTTTTC-CTCAA
1 TTTTTCTCTTTT
76238 TT-TTCTCTTTT
1 TTTTTCTCTTTT
76249 TTTTT-TCAATTTT
1 TTTTTCTC--TTTT
*
76262 TCTTTTCGACTTTT
1 T-TTTTC-TCTTTT
76276 TTTTTCTCTTTT
1 TTTTTCTCTTTT
76288 TT
1 TT
76290 ATTTTATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
10 3 0.06
11 8 0.17
12 11 0.23
13 16 0.33
14 9 0.19
16 1 0.02
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:76241 original size:23 final size:20
Alignment explanation
Indices: 76215--76267 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 20
76205 ACTTTTGTCT
76215 TTTTCTCTTTCTTTTTTCCTCAA
1 TTTTCTCTTT-TTTTTT--TCAA
76238 TTTTCTCTTTTTTTTTTCAA
1 TTTTCTCTTTTTTTTTTCAA
76258 TTTT-TCTTTT
1 TTTTCTCTTTT
76268 CGACTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.20
20 8 0.27
22 6 0.20
23 10 0.33
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCTCTTTTTTTTTTCAA
Found at i:76249 original size:20 final size:19
Alignment explanation
Indices: 76222--76267 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
76212 TCTTTTTCTC
76222 TTTC-TTTTTTCCTCAATT
1 TTTCTTTTTTTCCTCAATT
**
76240 TTCTCTTTTTTTTTTCAATT
1 TT-TCTTTTTTTCCTCAATT
76260 TTTCTTTT
1 TTTCTTTT
76268 CGACTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 8 0.33
20 14 0.58
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTCTTTTTTTCCTCAATT
Found at i:76970 original size:6 final size:6
Alignment explanation
Indices: 76950--77013 Score: 51
Period size: 6 Copynumber: 10.3 Consensus size: 6
76940 AGTGTATAAT
* * *
76950 AAAATA AAACA-A AAAATA AAAATAAA AAAATGA AAAATG AAAA-G ATAATA
1 AAAATA AAA-ATA AAAATA AAAAT--A AAAAT-A AAAATA AAAATA AAAATA
77000 AAAATA AAAATA AA
1 AAAATA AAAATA AA
77014 TATACTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
5 5 0.10
6 30 0.62
7 7 0.15
8 6 0.12
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (6 bp):
AAAATA
Done.