Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007972.1 Kokia drynarioides strain JFW-HI SEQ_122621, 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: 25753
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:147 original size:30 final size:29
Alignment explanation
Indices: 111--270 Score: 135
Period size: 30 Copynumber: 5.4 Consensus size: 29
101 TCCATTTCAA
*
111 CCCCAAACTTTCTAAAAATTATGTTTTAGC
1 CCCCAAACTTTCCAAAAATTATGTTTT-GC
* *
141 CCCCAAACTTGCCAAAAATTATTTTTTGGC
1 CCCCAAACTTTCCAAAAATTATGTTTT-GC
* * *
171 CCTCGAACTTTCCAAAAATT-TGAATTTGAC
1 CCCCAAACTTTCCAAAAATTATG-TTTTG-C
* * *
201 TCTCAAACTTTCTAAAAATTATGTTTTGAC
1 CCCCAAACTTTCCAAAAATTATGTTTTG-C
* ** *
231 CCCTAAACTTTCC-AAAATTCAAATTTAGC
1 CCCCAAACTTTCCAAAAATT-ATGTTTTGC
260 CCCCAAACTTT
1 CCCCAAACTTT
271 AAATTTTTTT
Statistics
Matches: 105, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
29 19 0.18
30 84 0.80
31 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (29 bp):
CCCCAAACTTTCCAAAAATTATGTTTTGC
Found at i:574 original size:17 final size:17
Alignment explanation
Indices: 554--587 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
544 ATTTTTAAAA
554 AAAAATATTTTTTAATT
1 AAAAATATTTTTTAATT
* *
571 AAAATTGTTTTTTAATT
1 AAAAATATTTTTTAATT
588 TTCTTCAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
AAAAATATTTTTTAATT
Found at i:3071 original size:184 final size:182
Alignment explanation
Indices: 2700--3656 Score: 1111
Period size: 178 Copynumber: 5.3 Consensus size: 182
2690 GCAATAGAAT
* *
2700 AAAACTTTAGGTACCAAAATGGGAAAAATTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
* * *
2765 AAAT-TCATGTGTCATAATTTGATTGGTTTGAATTCCTTTTTCTTTTTTTTTAATGTGAGTTAAT
66 AAATGTCATGTGTCATAATTTGATTGGTTTGGATT-C---TT-TTTTTTTTTAACGTGAGTTAAC
* * ** * * **
2829 AGCTGATACCTAAAGTGGTAGCAAAATAAAACTTTAAGT-TCCTACTTT-G-ATTAAA
126 AGTTGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTAT-CTACTTTGGTAAAAAA
* * * *
2884 AAAACTTTAGGCACCTAACTGGGAAAAGTTGCTTAGTTTAAGTACCTAAAGTGGGAATAGATTAA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
** * *
2949 AAATGTCACATGTCATAATTTGATTGGTTTGAATTCTTTTTTTTTTGGTAACGTGAGTTAACCGT
66 AAATGTCATGTGTCATAATTTGATTGGTTTGGATTCTTTTTTTTTT--TAACGTGAGTTAACAGT
* * * *
3014 TGCTACCTAAAGTGGCAACAGGATAAAACTTTAGGTATCTACTTTGGTAAAAAA
129 TGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGTAAAAAA
* * * * *
3068 AAAACTTTAAGTACTTAAATGAGAAAAGTTGCATAGTTTAAATACCTAAAGTGATAATAGATTAA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
* * * * *
3133 AAATGTCATGTGTCATGATTCGATTGGTTCGGATTC----TTTTTTAAACATGAGTTAACAGTTG
66 AAATGTCATGTGTCATAATTTGATTGGTTTGGATTCTTTTTTTTTTTAACGTGAGTTAACAGTTG
* *
3194 GTTCCTAAAGTGGTAATAGAATAAAACTTTGGGTATCTACTTTGGTAAAAAA
131 GTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGTAAAAAA
* *
3246 AAAACTTTAGGTACCTAAATGGGAGAAA-TTGCATAGTTTAAGTACCTAAAGTGGTAACAAATTA
1 AAAACTTTAGGTACCTAAATGGGA-AAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTA
* * * *
3310 AAAATATAATGTGTCATAATTTGATTGGTTTGGATTC----TTTTTTTAACATGAGTTAACTGTT
65 AAAATGTCATGTGTCATAATTTGATTGGTTTGGATTCTTTTTTTTTTTAACGTGAGTTAACAGTT
* *
3371 GGTACCTAAAGTGGTAATAAAATAAAACTTTAGGTATCTACTTTGGT-TAAAA
130 GGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGTAAAAAA
* * * * *
3423 AAAA-TATTAGGTACTTAAATGGGAAAAGTTGCATAGTTTAATTATCTAAAGTGGTAATAAAATA
1 AAAACT-TTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTA
* *
3487 AAATTGTCATTTGTCATAATTT-ATTTGGTTTGGATTCTTTTTTTTTTTTAAACGTGAGTTAACA
65 AAAATGTCATGTGTCATAATTTGA-TTGGTTTGGATTC-TTTTTTTTTTT-AACGTGAGTTAACA
* * * *
3551 ATTGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGCACCTACTTTGATAAAAAAAAA
127 GTTGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGT---AAAAAA
* * * *
3610 AAAAATTTAGATACCTAAATGAGAAAGGTT-CATAGTTTAAGTACCTA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTA
3657 TTTTGATATT
Statistics
Matches: 667, Mismatches: 85, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
176 5 0.01
177 88 0.13
178 213 0.32
179 3 0.00
180 14 0.02
181 2 0.00
182 57 0.09
183 59 0.09
184 154 0.23
185 28 0.04
186 15 0.02
187 28 0.04
188 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (182 bp):
AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
AAATGTCATGTGTCATAATTTGATTGGTTTGGATTCTTTTTTTTTTTAACGTGAGTTAACAGTTG
GTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGTAAAAAA
Found at i:7563 original size:27 final size:27
Alignment explanation
Indices: 7402--7561 Score: 117
Period size: 27 Copynumber: 5.9 Consensus size: 27
7392 CTTATAACCC
* * *
7402 CGTGTTTA-TGGTCCCGATGGACTATCT
1 CGTGTTTACT-GTCTCGACGGACTACCT
* * **
7429 CATGTTTACTATCTCGGTGGACTACCT
1 CGTGTTTACTGTCTCGACGGACTACCT
* * *
7456 CGTGTTTACTGTTTCAATGGACTACCT
1 CGTGTTTACTGTCTCGACGGACTACCT
* * * * *
7483 TGTGTTTATTGTCTTGACAGACTATCT
1 CGTGTTTACTGTCTCGACGGACTACCT
* * * *
7510 CATGTTTACTATCTCGGCGAACTACAC-
1 CGTGTTTACTGTCTCGACGGACTAC-CT
7537 CGTGTTTACTGTCTCGACGGACTAC
1 CGTGTTTACTGTCTCGACGGACTAC
7562 ACTAGTTGCC
Statistics
Matches: 100, Mismatches: 31, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
27 98 0.98
28 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.38
Consensus pattern (27 bp):
CGTGTTTACTGTCTCGACGGACTACCT
Found at i:11311 original size:17 final size:18
Alignment explanation
Indices: 11279--11312 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11269 AATTTCTATC
11279 CAATTTATACCCTAATTT
1 CAATTTATACCCTAATTT
*
11297 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
11313 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
CAATTTATACCCTAATTT
Found at i:11770 original size:32 final size:32
Alignment explanation
Indices: 11734--11795 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
11724 TTTAACCCTG
* * *
11734 TTCTTCTATTCCTTCTTTTGTTTCTTTTTTTT
1 TTCTTCTATTCATTCTTTTATATCTTTTTTTT
* *
11766 TTCTTTTATTTATTCTTTTATATCTTTTTT
1 TTCTTCTATTCATTCTTTTATATCTTTTTT
11796 ATATATATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.76
Consensus pattern (32 bp):
TTCTTCTATTCATTCTTTTATATCTTTTTTTT
Found at i:11784 original size:20 final size:20
Alignment explanation
Indices: 11746--11784 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11736 CTTCTATTCC
* * *
11746 TTCTTTTGTTTCTTTTTTTT
1 TTCTTTTATTTATTCTTTTT
11766 TTCTTTTATTTATTCTTTT
1 TTCTTTTATTTATTCTTTT
11785 ATATCTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (20 bp):
TTCTTTTATTTATTCTTTTT
Found at i:12588 original size:9 final size:9
Alignment explanation
Indices: 12576--12642 Score: 66
Period size: 9 Copynumber: 7.2 Consensus size: 9
12566 TTTTATTATT
12576 TTTTAATAA
1 TTTTAATAA
12585 TTTTAATAA
1 TTTTAATAA
*
12594 TTTCATATAA
1 TTTTA-ATAA
12604 TTCTTAATAA
1 TT-TTAATAA
12614 TGTTTAA-ATA
1 T-TTTAATA-A
*
12624 TTTTTAT-A
1 TTTTAATAA
12632 TTTTAATAA
1 TTTTAATAA
12641 TT
1 TT
12643 ATTTGAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
8 7 0.15
9 21 0.44
10 17 0.35
11 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (9 bp):
TTTTAATAA
Found at i:12588 original size:10 final size:10
Alignment explanation
Indices: 12555--12642 Score: 62
Period size: 10 Copynumber: 9.2 Consensus size: 10
12545 ATGGACATTG
*
12555 TTTTTAACAA
1 TTTTTAATAA
* *
12565 TTTTTATTAT
1 TTTTTAATAA
12575 TTTTTAATAA
1 TTTTTAATAA
12585 -TTTTAATAA
1 TTTTTAATAA
*
12594 -TTTCATATAA
1 TTTTTA-ATAA
*
12604 TTCTTAATAA
1 TTTTTAATAA
*
12614 TGTTTAA-ATA
1 TTTTTAATA-A
12624 TTTTT-AT-A
1 TTTTTAATAA
12632 -TTTTAATAA
1 TTTTTAATAA
12641 TT
1 TT
12643 ATTTGAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
7 4 0.07
8 3 0.05
9 16 0.27
10 34 0.57
11 3 0.05
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:13028 original size:26 final size:26
Alignment explanation
Indices: 12999--13050 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
12989 CATATTTTGC
*
12999 ATATTTTTATGATAATAATTTAAATT
1 ATATTTTTATCATAATAATTTAAATT
13025 ATATTTTTATCATAATAATTTAAATT
1 ATATTTTTATCATAATAATTTAAATT
13051 TTATACAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
ATATTTTTATCATAATAATTTAAATT
Found at i:14762 original size:17 final size:17
Alignment explanation
Indices: 14731--14793 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
14721 GGCCCAACAG
* *
14731 AATTTAAATTCATTTTA
1 AATTTAAGTTTATTTTA
*
14748 AAATTAAGTTTATTTTA
1 AATTTAAGTTTATTTTA
*
14765 AATTTAAGTTTATTATA
1 AATTTAAGTTTATTTTA
*
14782 AATTTAAATTTA
1 AATTTAAGTTTA
14794 AATTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTAAGTTTATTTTA
Found at i:14787 original size:23 final size:22
Alignment explanation
Indices: 14761--14806 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
14751 TTAAGTTTAT
*
14761 TTTAAATTTAAGTTTATTATAAA
1 TTTAAATTTAAATTTATT-TAAA
14784 TTTAAATTTAAATTTATTTAAA
1 TTTAAATTTAAATTTATTTAAA
14806 T
1 T
14807 AATACCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTAAATTTAAATTTATTTAAA
Found at i:15435 original size:2 final size:2
Alignment explanation
Indices: 15428--15457 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15418 TTTTAAACAC
15428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15458 TAAATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15525 original size:11 final size:10
Alignment explanation
Indices: 15509--15567 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 10
15499 TCAAACACGC
15509 ATTAAATACAT
1 ATTAAATA-AT
15520 ATTAAAT-AT
1 ATTAAATAAT
15529 ATTAAATAAT
1 ATTAAATAAT
*
15539 TTTATTAATAAT
1 ATTA--AATAAT
15551 ATTAGTAATAAT
1 ATTA--AATAAT
15563 ATTAA
1 ATTAA
15568 TAACAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
9 9 0.21
10 6 0.14
11 7 0.17
12 20 0.48
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (10 bp):
ATTAAATAAT
Found at i:15776 original size:32 final size:32
Alignment explanation
Indices: 15738--15800 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
15728 ATAAGGAAAG
* * *
15738 AACAGATTTGAGATTAAGAAATAAAAA-TAAAA
1 AACAGATTTCAAATTAA-AAAAAAAAACTAAAA
15770 AACAGATTTCAAATTAAAAAAAAAAACTAAA
1 AACAGATTTCAAATTAAAAAAAAAAACTAAA
15801 TAGATTCGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (32 bp):
AACAGATTTCAAATTAAAAAAAAAAACTAAAA
Found at i:16748 original size:59 final size:59
Alignment explanation
Indices: 16664--17006 Score: 315
Period size: 59 Copynumber: 5.9 Consensus size: 59
16654 CCAAATGTAA
* * * * *
16664 AAAAATTCCA-TTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCCCGGATGACC
1 AAAAATTTCATTTTTGATCCCGAACCTTCCAAAAATTACCATTTTACCCCCAGATGACC
** * * * *
16722 AAAAATTTTGTTTTTAATCCCGAACCTTCCAAAAATTACCAATTTACCCCTAAAT-ATCC
1 AAAAATTTCATTTTTGATCCCGAACCTTCCAAAAATTACCATTTTACCCCCAGATGA-CC
* * *
16781 AAAAATTTCATTTTTGA-CTTCGAA-CTTCCCAAAAATTACCATTTTACCCCCACATGTCC
1 AAAAATTTCATTTTTGATC-CCGAACCTT-CCAAAAATTACCATTTTACCCCCAGATGACC
* * * * * * * *
16840 AAAAA-TTCATTTTTGATCCTGAACTTTCCAAAAATTATCATTGTACCCTCGGATGTCT
1 AAAAATTTCATTTTTGATCCCGAACCTTCCAAAAATTACCATTTTACCCCCAGATGACC
* ** *
16898 AAAAATTTCATTTTTGATCTCGAATTTTCCAAAAATTACCATTTTACCCCCAAAT-ATCC
1 AAAAATTTCATTTTTGATCCCGAACCTTCCAAAAATTACCATTTTACCCCCAGATGA-CC
* * ** *
16957 AAAAATTCCA-TTTTGACCCCGAACCTT-CAAAAATTAGTATTTTGCCCCCA
1 AAAAATTTCATTTTTGATCCCGAACCTTCCAAAAATTACCATTTTACCCCCA
17007 AAGTGTCCAA
Statistics
Matches: 232, Mismatches: 44, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
57 20 0.09
58 69 0.30
59 143 0.62
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (59 bp):
AAAAATTTCATTTTTGATCCCGAACCTTCCAAAAATTACCATTTTACCCCCAGATGACC
Found at i:16793 original size:117 final size:116
Alignment explanation
Indices: 16664--16992 Score: 337
Period size: 117 Copynumber: 2.8 Consensus size: 116
16654 CCAAATGTAA
* * * * **
16664 AAAAATTCCA-TTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCCCGGATGACCAAAAAT
1 AAAAATTTCATTTTTGACCTCGAA-CTTCCAAAAATTACCATTTTACCCCCACATGACCAAAAA-
**
16728 TTTGTTTTTAATCCCGAACCTTCCAAAAATTACCAATT-TACCC-CTAAATATCC
64 TTCATTTTTAATCCCGAACCTTCCAAAAATTACC-ATTGTACCCTC-AAATATCC
* *
16781 AAAAATTTCATTTTTGACTTCGAACTTCCCAAAAATTACCATTTTACCCCCACATGTCCAAAAAT
1 AAAAATTTCATTTTTGACCTCGAACTT-CCAAAAATTACCATTTTACCCCCACATGACCAAAAAT
* * * * ** * *
16846 TCATTTTTGATCCTGAACTTTCCAAAAATTATCATTGTACCCTCGGATGTCT
65 TCATTTTTAATCCCGAACCTTCCAAAAATTACCATTGTACCCTCAAATATCC
* * *
16898 AAAAATTTCATTTTTGATCTCGAATTTTCCAAAAATTACCATTTTACCCCCAAAT-ATCCAAAAA
1 AAAAATTTCATTTTTGACCTCGAA-CTTCCAAAAATTACCATTTTACCCCCACATGA-CCAAAAA
* *
16962 TTCCA-TTTTGACCCCGAACCTT-CAAAAATTA
64 TT-CATTTTTAATCCCGAACCTTCCAAAAATTA
16993 GTATTTTGCC
Statistics
Matches: 179, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
116 12 0.07
117 120 0.67
118 47 0.26
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.33
Consensus pattern (116 bp):
AAAAATTTCATTTTTGACCTCGAACTTCCAAAAATTACCATTTTACCCCCACATGACCAAAAATT
CATTTTTAATCCCGAACCTTCCAAAAATTACCATTGTACCCTCAAATATCC
Found at i:16842 original size:29 final size:28
Alignment explanation
Indices: 16809--17031 Score: 96
Period size: 29 Copynumber: 7.7 Consensus size: 28
16799 TTCGAACTTC
16809 CCAAAAATTACCATTTTACCCCCACATGT
1 CCAAAAATTACCATTTTACCCCCA-ATGT
* ** *
16838 CCAAAAATT--CATTTTTGATCCTGAACTTT
1 CCAAAAATTACCA-TTTT-ACCCCCAA-TGT
* * **
16867 CCAAAAATTATCATTGTACCCTCGGATGT
1 CCAAAAATTACCATTTTACCC-CCAATGT
* * * * * *
16896 CTAAAAATT-TCATTTTTGATCTCGAATTTT
1 CCAAAAATTACCA-TTTT-ACCCCCAA-TGT
*
16926 CCAAAAATTACCATTTTACCCCCAAATAT
1 CCAAAAATTACCATTTTACCCCC-AATGT
* **
16955 CCAAAAATT-CCATTTTGACCCCGAACCT
1 CCAAAAATTACCATTTT-ACCCCCAATGT
* ** *
16983 TCAAAAATTAGTATTTTGCCCCCAAAGTGT
1 CCAAAAATTACCATTTTACCCCC-AA-TGT
*
17013 CC-AAAATTACTATTTTACC
1 CCAAAAATTACCATTTTACC
17032 TCGAGCATCC
Statistics
Matches: 145, Mismatches: 34, Indels: 30
0.69 0.16 0.14
Matches are distributed among these distances:
27 2 0.01
28 30 0.21
29 84 0.58
30 25 0.17
31 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.34
Consensus pattern (28 bp):
CCAAAAATTACCATTTTACCCCCAATGT
Found at i:17028 original size:117 final size:114
Alignment explanation
Indices: 16632--17020 Score: 331
Period size: 117 Copynumber: 3.3 Consensus size: 114
16622 TCCCTAAACT
* ** * * ** *
16632 TTCC-AAAATTATTATTTTAACCCCAAATGTAAAAAAATTCCA-TTTTAACCCCGAACCTT-CTA
1 TTCCAAAAATTA-TATTTTACCCCCAAATGT-CCAAAATTTCATTTTTGACTTCGAA-CTTCCCA
** ** *
16694 AAAATTACCATTTTACCCCCGGATGA-CCAAAAATTTTGTTTTTAATCCCGAACC
63 AAAATTACCATTTTACCCCCAAAT-ATCCAAAAA--TTCATTTTGATCCCGAACC
* * * *
16748 TTCCAAAAATTACCAATTTACCCCTAAATATCCAAAAATTTCATTTTTGACTTCGAACTTCCCAA
1 TTCCAAAAATTA-TATTTTACCCCCAAATGTCC-AAAATTTCATTTTTGACTTCGAACTTCCCAA
* * * *
16813 AAATTACCATTTTACCCCCACATGTCCAAAAATTCATTTTTGATCCTGAACT
64 AAATTACCATTTTACCCCCAAATATCCAAAAATTCA-TTTTGATCCCGAACC
* * ** * * *
16865 TTCCAAAAATTATCATTGTACCCTCGGATGTCTAAAAATTTCATTTTTGA-TCTCGAATTTTCCA
1 TTCCAAAAATTAT-ATTTTACCCCCAAATGTC-CAAAATTTCATTTTTGACT-TCGAACTTCCCA
*
16929 AAAATTACCATTTTACCCCCAAATATCCAAAAATTCCATTTTGACCCCGAACC
63 AAAATTACCATTTTACCCCCAAATATCCAAAAATT-CATTTTGATCCCGAACC
*
16982 TT-CAAAAATTAGTATTTTGCCCCCAAAGTGTCCAAAATT
1 TTCCAAAAATTA-TATTTTACCCCCAAA-TGTCCAAAATT
17021 ACTATTTTAC
Statistics
Matches: 218, Mismatches: 43, Indels: 24
0.76 0.15 0.08
Matches are distributed among these distances:
116 31 0.14
117 144 0.66
118 43 0.20
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (114 bp):
TTCCAAAAATTATATTTTACCCCCAAATGTCCAAAATTTCATTTTTGACTTCGAACTTCCCAAAA
ATTACCATTTTACCCCCAAATATCCAAAAATTCATTTTGATCCCGAACC
Found at i:17045 original size:57 final size:57
Alignment explanation
Indices: 16636--17047 Score: 247
Period size: 59 Copynumber: 7.1 Consensus size: 57
16626 TAAACTTTCC
** * * ** * * *
16636 AAAATTATTATTTTAACCCCAAATGTAAAAAAATTCCATTTTAACCCCGAACCTTCTA
1 AAAATTACCATTTTACCCCCAAATATCCAAAAATTCCATTTTGACCCCGAA-CATCCA
** *** * * *
16694 AAAATTACCATTTTACCCCCGGATGA-CCAAAAATTTTGTTTTTAATCCCGAACCTTCCA
1 AAAATTACCATTTTACCCCCAAAT-ATCCAAAAA-TTCCATTTTGACCCCGAA-CATCCA
* * * ** *
16753 AAAATTACCAATTTACCCCTAAATATCCAAAAATTTCATTTTTGACTTCGAACTTCCCA
1 AAAATTACCATTTTACCCCCAAATATCCAAAAATTCCA-TTTTGACCCCGAACAT-CCA
* * * * *
16812 AAAATTACCATTTTACCCCCACATGTCCAAAAATT-CATTTTTGATCCTGAACTTTCCA
1 AAAATTACCATTTTACCCCCAAATATCCAAAAATTCCA-TTTTGACCCCGAAC-ATCCA
* * * ** * * * * * **
16870 AAAATTATCATTGTACCCTCGGATGTCTAAAAATTTCATTTTTGATCTCGAATTTTCCA
1 AAAATTACCATTTTACCCCCAAATATCCAAAAATTCCA-TTTTGACCCCGAA-CATCCA
* *
16929 AAAATTACCATTTTACCCCCAAATATCCAAAAATTCCATTTTGACCCCGAACCTTCA
1 AAAATTACCATTTTACCCCCAAATATCCAAAAATTCCATTTTGACCCCGAACATCCA
** * * * * *
16986 AAAATTAGTATTTTGCCCCCAAAGTGTCC-AAAATTACTATTTT-ACCTCGAGCATCCA
1 AAAATTACCATTTTACCCCCAAA-TATCCAAAAATT-CCATTTTGACCCCGAACATCCA
17043 AAAAT
1 AAAAT
17048 CGCATTTTGA
Statistics
Matches: 282, Mismatches: 62, Indels: 21
0.77 0.17 0.06
Matches are distributed among these distances:
57 44 0.16
58 97 0.34
59 141 0.50
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.33
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCAAATATCCAAAAATTCCATTTTGACCCCGAACATCCA
Found at i:25638 original size:21 final size:19
Alignment explanation
Indices: 25614--25669 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 19
25604 TTTTACCCAA
25614 AAAAAATAGAGAAAAGAAAAT
1 AAAAAA-AGA-AAAAGAAAAT
*
25635 AAAAGAAAAGAAAAAGGAAAT
1 -AAA-AAAAGAAAAAGAAAAT
25656 AGAAAAAAGAAAAA
1 A-AAAAAAGAAAAA
25670 AGGAGAGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 11 0.35
21 11 0.35
22 6 0.19
23 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAAAAAGAAAAAGAAAAT
Found at i:25670 original size:21 final size:21
Alignment explanation
Indices: 25613--25673 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
25603 CTTTTACCCA
* *
25613 AAAAAAATAGAGAAAAGAAAAT
1 AAAAAAA-AGAAAAAAGGAAAT
25635 AAAAGAAAAG-AAAAAGGAAAT
1 AAAA-AAAAGAAAAAAGGAAAT
*
25656 AGAAAAAAGAAAAAAGGA
1 AAAAAAAAGAAAAAAGGA
25674 GAGGTCAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.15
21 20 0.59
22 6 0.18
23 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAGGAAAT
Done.