Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013677.1 Kokia drynarioides strain JFW-HI SEQ_128705, 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: 390591
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 52 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:340794 original size:58 final size:58
Alignment explanation
Indices: 340699--340880 Score: 204
Period size: 58 Copynumber: 3.1 Consensus size: 58
340689 TAGTTCTATT
* * * * * *
340699 ACTGTTCTCCAAAATTTTACACTTTTGCCACAATTTTTCCATATTTTACAATTCTACC
1 ACTGTTTTCCAGAATTTTACAGTTTTGCCACAGTTTTTCCAAATTTTACAATTTTACC
* * * * * **
340757 ACTATTTTCCATAATTTTATAGTTTT-CTCATAGTTTTTCCAAATTTTACAGTTTTGTC
1 ACTGTTTTCCAGAATTTTACAGTTTTGC-CACAGTTTTTCCAAATTTTACAATTTTACC
* * *
340815 ATTGCTTTCCAGAATTTTACAGTTTTGCCACAGTTTTTCCAGATTTTACAATTTTACC
1 ACTGTTTTCCAGAATTTTACAGTTTTGCCACAGTTTTTCCAAATTTTACAATTTTACC
340873 ACTGTTTT
1 ACTGTTTT
340881 TAAGATTTTA
Statistics
Matches: 98, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
57 1 0.01
58 96 0.98
59 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (58 bp):
ACTGTTTTCCAGAATTTTACAGTTTTGCCACAGTTTTTCCAAATTTTACAATTTTACC
Found at i:340879 original size:29 final size:29
Alignment explanation
Indices: 340627--340892 Score: 147
Period size: 29 Copynumber: 9.3 Consensus size: 29
340617 AGTTTTCTCT
*
340627 ATTTTACAGTTCTGCCACTGCTTTTT--AG
1 ATTTTACAGTTTTGCCACTG-TTTTTCCAG
*
340655 ATTTTACAATTTTGCCACTAG-TTTT-CAG
1 ATTTTACAGTTTTGCCACT-GTTTTTCCAG
** * *** * *
340683 ATTTTTTAGTTCTATTACTG-TTCTCCAAA
1 ATTTTACAGTTTTGCCACTGTTTTTCC-AG
* ** *
340712 ATTTTACACTTTTGCCACAATTTTTCCAT
1 ATTTTACAGTTTTGCCACTGTTTTTCCAG
* * * * *
340741 ATTTTACAATTCTACCACT-ATTTTCCATA
1 ATTTTACAGTTTTGCCACTGTTTTTCCA-G
* *
340770 ATTTTATAGTTTT-CTCA-TAGTTTTTCCAA
1 ATTTTACAGTTTTGC-CACT-GTTTTTCCAG
* * *
340799 ATTTTACAGTTTTGTCATTG-CTTTCCAG
1 ATTTTACAGTTTTGCCACTGTTTTTCCAG
*
340827 AATTTTACAGTTTTGCCACAGTTTTTCCAG
1 -ATTTTACAGTTTTGCCACTGTTTTTCCAG
* * *
340857 ATTTTACAATTTTACCACTGTTTTT-AAG
1 ATTTTACAGTTTTGCCACTGTTTTTCCAG
340885 ATTTTACA
1 ATTTTACA
340893 ATATTTCCAT
Statistics
Matches: 181, Mismatches: 44, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
27 8 0.04
28 57 0.31
29 96 0.53
30 20 0.11
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.48
Consensus pattern (29 bp):
ATTTTACAGTTTTGCCACTGTTTTTCCAG
Found at i:340908 original size:28 final size:28
Alignment explanation
Indices: 340828--340909 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
340818 GCTTTCCAGA
* * *
340828 ATTTTACAGTTTTGCCAC-AGTTTTTCCAG
1 ATTTTACAATTTTACCACTA-TTTTT-AAG
*
340857 ATTTTACAATTTTACCACTGTTTTTAAG
1 ATTTTACAATTTTACCACTATTTTTAAG
*
340885 ATTTTACAATATTT-CCATTATTTTT
1 ATTTTACAAT-TTTACCACTATTTTT
340910 CAAAAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 21 0.47
29 24 0.53
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (28 bp):
ATTTTACAATTTTACCACTATTTTTAAG
Found at i:340922 original size:116 final size:116
Alignment explanation
Indices: 340706--340927 Score: 272
Period size: 116 Copynumber: 1.9 Consensus size: 116
340696 ATTACTGTTC
*
340706 TCCAAAATTTTACACTTTTGCCACAATTTTTCCATATTTTACAATTCTACCACTATTTTCCATAA
1 TCCAAAATTTTACACTTTTGCCACAATTTTTCCAGATTTTACAATTCTACCACTATTTTCCATAA
* * * **
340771 TTTTATAGTTTTCTCATAGTTTTTCCAAATTTTACAGTTTTGTCATTGCTT
66 TTTTACAATTTTCTCATAGTTTTTCAAAAAATTACAGTTTTGTCATTGCTT
* * * * * *
340822 TCCAGAATTTTACAGTTTTGCCACAGTTTTTCCAGATTTTACAATTTTACCACTGTTTT-TA-AG
1 TCCAAAATTTTACACTTTTGCCACAATTTTTCCAGATTTTACAATTCTACCACTATTTTCCATA-
340885 ATTTTACAATATTTC-CATTA-TTTTTCAAAAAAATTACAGTTTT
65 ATTTTACAAT-TTTCTCA-TAGTTTTTC-AAAAAATTACAGTTTT
340928 ACTATAACCT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
114 1 0.01
115 17 0.19
116 72 0.80
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (116 bp):
TCCAAAATTTTACACTTTTGCCACAATTTTTCCAGATTTTACAATTCTACCACTATTTTCCATAA
TTTTACAATTTTCTCATAGTTTTTCAAAAAATTACAGTTTTGTCATTGCTT
Found at i:342011 original size:40 final size:40
Alignment explanation
Indices: 341966--342098 Score: 221
Period size: 40 Copynumber: 3.3 Consensus size: 40
341956 ATAGGTTCAT
*
341966 AAGTCTTCCTTTTAATCAATCTTATGCTCTACCGAGTCAC
1 AAGTCTTCCTTTTAATCACTCTTATGCTCTACCGAGTCAC
*
342006 AAGTCTTCCTTTTAATCACTCTTATGCTCTATCGAGTCAC
1 AAGTCTTCCTTTTAATCACTCTTATGCTCTACCGAGTCAC
* * *
342046 AAGTCTTCCTTTCAATCACTCTTATGCTCTACTGAGTCAT
1 AAGTCTTCCTTTTAATCACTCTTATGCTCTACCGAGTCAC
342086 AAGTCTTCCTTTT
1 AAGTCTTCCTTTT
342099 TAAAAACAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 86 1.00
ACGTcount: A:0.23, C:0.27, G:0.10, T:0.41
Consensus pattern (40 bp):
AAGTCTTCCTTTTAATCACTCTTATGCTCTACCGAGTCAC
Found at i:342171 original size:41 final size:43
Alignment explanation
Indices: 342124--342229 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 43
342114 CGCTCATTTT
* * * **
342124 GAGACATGAGTTTTCCTTTAATAT-AA-TCTCATTCTTATCCC
1 GAGACATGAGTCTTCCTTTAATATAAATTCTCATGCTCAAACC
*
342165 GAGACATGAGTCTTCCTTTTATATAAATTCTCATGCTCAAACC
1 GAGACATGAGTCTTCCTTTAATATAAATTCTCATGCTCAAACC
342208 GAGACATGAGTCTTCCATTTAA
1 GAGACATGAGTCTTCC-TTTAA
342230 ATATTGAGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
41 22 0.40
42 2 0.04
43 27 0.49
44 4 0.07
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (43 bp):
GAGACATGAGTCTTCCTTTAATATAAATTCTCATGCTCAAACC
Found at i:343487 original size:498 final size:497
Alignment explanation
Indices: 342223--343720 Score: 2577
Period size: 499 Copynumber: 3.0 Consensus size: 497
342213 ATGAGTCTTC
342223 CATTTAAATATTGAGTTTCTCAAATAAATTCTCAATAGATAAAAATTAGTAGTTCAAATATAAAA
1 CATTTAAATATTGAGTTTCTCAAATAAATTCTCAATAGATAAAAATTAGTAGTTCAAATATAAAA
* **
342288 CGTAACTAACAAACTTATTAGATGAAATTGTAGTTTAGGTGAAACTTCAGGGACTATTCTATGAT
66 CGTAACAAACAAACTTATCGGATGAAATTGTAGTTTAGGTGAAACTTCAGGGACTATTCTATGAT
* * * * *
342353 TTTCCCCTATCCACAATCTATGGCCCGATCTTGATCTATCATAAAATAAATCAATTCTCTCATTA
131 TTT-CCCTGTCCACGATCTGTGGCCCGATCTTGATCTATCACAAAATAAATCAATTCTCCCATTA
342418 AATCATATAATTTAATCAATTTACACATATAAGTCCTTTTTTGAAAAAATTACGAAATTACTCCT
195 AATCATATAATTTAATCAATTTACACATATAAGTCCTTTTTTGAAAAAATTACGAAATTACTCCT
* * *
342483 AAACTTTGTATTTCTATTCAATTTAGTCCTTATAGCCAAAACATGTAAAGTAACCATTTCTAAAT
260 AAACTTTATATTTCTATTCAATTTAGTCCTTAGAGCCAAAACATGTAAAATAACCATTTCTAAAT
*
342548 TTACCCATTGCCAACCAAATATTCTAGGACAAAATCTCAACTAATTCATACATCTATTTCACATC
325 TTACCCATTGCCAACCAAATATTCTAGGACAAAATCTCAACTCATTCATACATCTATTTCACATC
*
342613 AAGA-ATGTACTTTTACCATTTTCACAATCTAGTCCTTAAACCCTAAATTCATAAAAAAATCACT
390 AAGACATGTACTTTTACCATTTTTACAATCTAGTCCTTAAACCCTAAATTCAT-AAAAAATCACT
342677 TTACATGTTAAACCCAATCTTCAAGCTTTCAAATCTTCCGTAAA
454 TTACATGTTAAACCCAATCTTCAAGCTTTCAAATCTTCCGTAAA
* *
342721 CATTTAAATATCGAGTTTCTCAAAATACATTCTCAATAGATAAAAATTAGTAGTTCAAATATAAA
1 CATTTAAATATTGAGTTTCTC-AAATAAATTCTCAATAGATAAAAATTAGTAGTTCAAATATAAA
* ** *
342786 ACGTAACAAACAAACTTATCGAACAAAATTATAGTTTAGGTGAAACTTCAGGGACTATTCTATGA
65 ACGTAACAAACAAACTTATCGGATGAAATTGTAGTTTAGGTGAAACTTCAGGGACTATTCTATGA
* *
342851 TATTTCCCTGTCCGCGATATGTGGCCCGATCTTGATCTATCACAAAATAAATCAATTCTCCCATT
130 T-TTTCCCTGTCCACGATCTGTGGCCCGATCTTGATCTATCACAAAATAAATCAATTCTCCCATT
*
342916 AAATCATATAATTTAATCAATTTACACATATAAGTCCTTTTTTGAAAAAATTATGAAATTACTCC
194 AAATCATATAATTTAATCAATTTACACATATAAGTCCTTTTTTGAAAAAATTACGAAATTACTCC
* *
342981 TAAACTTTATATTTCTATTCAATTTAGTCCTTGGAGCCAAAACATGTAAAATAACTATTTCTAAA
259 TAAACTTTATATTTCTATTCAATTTAGTCCTTAGAGCCAAAACATGTAAAATAACCATTTCTAAA
* * *
343046 TTTACCCATTGCCAACCAAATAATCTAGGACAAAATATTAACTCATTCATACATCTATTTCACAT
324 TTTACCCATTGCCAACCAAATATTCTAGGACAAAATCTCAACTCATTCATACATCTATTTCACAT
*
343111 CAAGACATGTACTTTTACCATTTTTACAGTCTAGTCCTTAAACCCTAAATTCATAAAAAATCACT
389 CAAGACATGTACTTTTACCATTTTTACAATCTAGTCCTTAAACCCTAAATTCATAAAAAATCACT
* *
343176 TTGCATGTTAAACCCAATCTTCAAGCTTTCAAATCTTTCGTAAA
454 TTACATGTTAAACCCAATCTTCAAGCTTTCAAATCTTCCGTAAA
* *
343220 CATTTAAATATTGAGTTTCTCAAATATATTCTTAATAGATAAAAATTAGTAGTTCAAATATAAAA
1 CATTTAAATATTGAGTTTCTCAAATAAATTCTCAATAGATAAAAATTAGTAGTTCAAATATAAAA
*
343285 CGTAACAAACAAACTTATCGGATGAAATTGTAGTTTAGGTGAAACTTCAAGGACTATTCTATGAT
66 CGTAACAAACAAACTTATCGGATGAAATTGTAGTTTAGGTGAAACTTCAGGGACTATTCTATGAT
343350 TTTCCCTTGTCCACGATCTGTGGCCCGATCTTGATCTATCACAAAATAAATCAATTCTCCCATTA
131 TTTCCC-TGTCCACGATCTGTGGCCCGATCTTGATCTATCACAAAATAAATCAATTCTCCCATTA
**
343415 AATCATATAATTTAATCAATTTACACATATAAGTATTTTTTTGAAAAAATTACGAAATTACTCCT
195 AATCATATAATTTAATCAATTTACACATATAAGTCCTTTTTTGAAAAAATTACGAAATTACTCCT
*
343480 AAACTTTATATTTCTATTCAATTTAGTCCTTAGAGCCAAAATATGTAAAATAACCATTTCTAAAT
260 AAACTTTATATTTCTATTCAATTTAGTCCTTAGAGCCAAAACATGTAAAATAACCATTTCTAAAT
*
343545 TTACCCATTGCCAACCAAATATTCTAGGACAAGATCTCAACTCATTCATACATCTATTTCACATC
325 TTACCCATTGCCAACCAAATATTCTAGGACAAAATCTCAACTCATTCATACATCTATTTCACATC
*
343610 AAGACATGTACTTTTACC-TTTTTACAATCTAGTCCTTAAACCCTAAATTCATCAAAAATCACTT
390 AAGACATGTACTTTTACCATTTTTACAATCTAGTCCTTAAACCCTAAATTCATAAAAAATCACTT
**
343674 TACATGTTAAACCCAATCTTCAAGCTTTCAAATCTTCAATAAA
455 TACATGTTAAACCCAATCTTCAAGCTTTCAAATCTTCCGTAAA
343717 CATT
1 CATT
343721 CAAAGACAAG
Statistics
Matches: 940, Mismatches: 56, Indels: 9
0.94 0.06 0.01
Matches are distributed among these distances:
497 93 0.10
498 381 0.41
499 417 0.44
500 49 0.05
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (497 bp):
CATTTAAATATTGAGTTTCTCAAATAAATTCTCAATAGATAAAAATTAGTAGTTCAAATATAAAA
CGTAACAAACAAACTTATCGGATGAAATTGTAGTTTAGGTGAAACTTCAGGGACTATTCTATGAT
TTTCCCTGTCCACGATCTGTGGCCCGATCTTGATCTATCACAAAATAAATCAATTCTCCCATTAA
ATCATATAATTTAATCAATTTACACATATAAGTCCTTTTTTGAAAAAATTACGAAATTACTCCTA
AACTTTATATTTCTATTCAATTTAGTCCTTAGAGCCAAAACATGTAAAATAACCATTTCTAAATT
TACCCATTGCCAACCAAATATTCTAGGACAAAATCTCAACTCATTCATACATCTATTTCACATCA
AGACATGTACTTTTACCATTTTTACAATCTAGTCCTTAAACCCTAAATTCATAAAAAATCACTTT
ACATGTTAAACCCAATCTTCAAGCTTTCAAATCTTCCGTAAA
Found at i:346798 original size:52 final size:52
Alignment explanation
Indices: 346688--346977 Score: 420
Period size: 52 Copynumber: 5.6 Consensus size: 52
346678 TGCGTATTTG
* * *
346688 ATACTCACGATGACACAGAGTCATCGGACCT-TTAATCCATAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* * *
346739 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCACAAAGGATTCTT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* *
346791 ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
** * * *
346843 ATACTCAAAATGAAACATAGTCATTGGACCTCATAATCCACAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* * *
346895 ATACTCACGAAGATACATAGTCATCGGACCTCATAATCCATGAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
*
346947 ATACTCACGATGACACATAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
346978 ATTTCATTTA
Statistics
Matches: 210, Mismatches: 28, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
51 29 0.14
52 181 0.86
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
Found at i:352663 original size:29 final size:28
Alignment explanation
Indices: 352559--352872 Score: 163
Period size: 29 Copynumber: 11.0 Consensus size: 28
352549 TACCACAGTT
* *
352559 TTTTTCA-ATTTTTACAATTTTACCACTGG
1 TTTTTCAGA-TTTTACAGTTTTGCCACT-G
* *
352588 TTTTCCAGATTTTACAGTTTTGCCATTG
1 TTTTTCAGATTTTACAGTTTTGCCACTG
* * * *
352616 TTTTTCAAAATTTATAGTTTTGCCATTGG
1 TTTTTCAGATTTTACAGTTTTGCCACT-G
* * *
352645 TTTTTTAGATTTTACAG-TTCGACCACTA
1 TTTTTCAGATTTTACAGTTTTG-CCACTG
* *
352673 TTTTTTAGAATTTTACAGTTTTGACA-TAG
1 TTTTTCAG-ATTTTACAGTTTTGCCACT-G
* * *
352702 TTTTTCCAGTTTTTACAATTCTGCCACT-
1 TTTTT-CAGATTTTACAGTTTTGCCACTG
* * * * * **
352730 ATTTTCTACTACTTTATAGTTTTCCCACAA
1 TTTTTC-A-GATTTTACAGTTTTGCCACTG
* * *
352760 TTTTTCTAGATTTTACAGTTCTACCGCT-
1 TTTTTC-AGATTTTACAGTTTTGCCACTG
* * *
352788 ATTTTCAAGATTTTTACAGTTTT-CTACAG
1 TTTTTC-AGA-TTTTACAGTTTTGCCACTG
* *
352817 TTTTTCCAGATTTTACAATTTTGCCATTG
1 TTTTT-CAGATTTTACAGTTTTGCCACTG
* * *
352846 TTTTTCATATTTTATAATTTTGCCACT
1 TTTTTCAGATTTTACAGTTTTGCCACT
352873 ATCTTTCAAA
Statistics
Matches: 216, Mismatches: 54, Indels: 31
0.72 0.18 0.10
Matches are distributed among these distances:
27 1 0.00
28 81 0.38
29 119 0.55
30 15 0.07
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.51
Consensus pattern (28 bp):
TTTTTCAGATTTTACAGTTTTGCCACTG
Found at i:352879 original size:28 final size:28
Alignment explanation
Indices: 352826--352880 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
352816 GTTTTTCCAG
* * *
352826 ATTTTACAATTTTGCCATTGTTTTTCAT
1 ATTTTACAATTTTGCCACTATCTTTCAT
*
352854 ATTTTATAATTTTGCCACTATCTTTCA
1 ATTTTACAATTTTGCCACTATCTTTCA
352881 AAAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (28 bp):
ATTTTACAATTTTGCCACTATCTTTCAT
Found at i:353213 original size:58 final size:56
Alignment explanation
Indices: 353134--353319 Score: 176
Period size: 58 Copynumber: 3.2 Consensus size: 56
353124 ATATATTTTT
* *
353134 AGATTTTACAGTTCTATCACTATTTTCTAGAATTTTACTGTTTTGACACAGTTTTTCC
1 AGATTTTACAATTCTACCACTATTTTCTAGAATTTTACTGTTTT--CACAGTTTTTCC
* * ** * * *
353192 AGTTTTTACAATTCTGCCACTATTTTCTACTACTTTA-TAGTTTTCCCACAATTTTTCT
1 AGATTTTACAATTCTACCACTATTTTCTAGAATTTTACT-GTTTT--CACAGTTTTTCC
* ** * * *
353250 AGATTTTACAGTTCTACTGCTATTTTCAAGATTTTTACAGTTTTCTACAGTTTTTCC
1 AGATTTTACAATTCTACCACTATTTTCTAGAATTTTACTGTTTTC-ACAGTTTTTCC
353307 AGATTTTACAATT
1 AGATTTTACAATT
353320 TTGCCATTGT
Statistics
Matches: 100, Mismatches: 25, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
56 1 0.01
57 22 0.22
58 77 0.77
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (56 bp):
AGATTTTACAATTCTACCACTATTTTCTAGAATTTTACTGTTTTCACAGTTTTTCC
Found at i:353274 original size:29 final size:27
Alignment explanation
Indices: 353242--353316 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
353232 TTTTCCCACA
* *
353242 ATTTTTCTAGATTTTACAGTTCTACTGC
1 ATTTTTCAAGATTTTACAGTT-TACTAC
*
353270 -TATTTTCAAGATTTTTACAGTTTTCTAC
1 AT-TTTTCAAGA-TTTTACAGTTTACTAC
*
353298 AGTTTTTCCAGATTTTACA
1 A-TTTTTCAAGATTTTACA
353317 ATTTTGCCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.03
28 19 0.49
29 18 0.46
30 1 0.03
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (27 bp):
ATTTTTCAAGATTTTACAGTTTACTAC
Found at i:353284 original size:28 final size:27
Alignment explanation
Indices: 353243--353316 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 27
353233 TTTCCCACAA
* *
353243 TTTTTCTAGATTTTACAG-TTCTACTG
1 TTTTTCAAGATTTTACAGTTTCTACAG
353269 CTATTTTCAAGATTTTTACAGTTTTCTACAG
1 -T-TTTTCAAGA-TTTTACAG-TTTCTACAG
*
353300 TTTTTCCAGATTTTACA
1 TTTTTCAAGATTTTACA
353317 ATTTTGCCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 1 0.03
28 15 0.38
29 16 0.40
30 1 0.03
31 7 0.17
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.51
Consensus pattern (27 bp):
TTTTTCAAGATTTTACAGTTTCTACAG
Found at i:353362 original size:28 final size:28
Alignment explanation
Indices: 353309--353363 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
353299 GTTTTTCCAG
* * *
353309 ATTTTACAATTTTGCCATTGTTTTTCAT
1 ATTTTACAATTTTGCCACTATCTTTCAT
*
353337 ATTTTATAATTTTGCCACTATCTTTCA
1 ATTTTACAATTTTGCCACTATCTTTCA
353364 AAAAAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (28 bp):
ATTTTACAATTTTGCCACTATCTTTCAT
Found at i:359417 original size:30 final size:29
Alignment explanation
Indices: 359319--359414 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
359309 AAAATTTCAA
* *
359319 GAAGTTTAAGGGTTGAATTTGAATTTTTG
1 GAAGTTTAAGGGTTAAATTTAAATTTTTG
* ** **
359348 GAAGTTTAAGGGTTAAAATCCAATTTTAA
1 GAAGTTTAAGGGTTAAATTTAAATTTTTG
* *
359377 GAAGTTTAGGGGTCAAATTTAAATTTTTG
1 GAAGTTTAAGGGTTAAATTTAAATTTTTG
359406 GAAAGTTTA
1 G-AAGTTTA
359415 GGGACTTACT
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
29 46 0.87
30 7 0.13
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.40
Consensus pattern (29 bp):
GAAGTTTAAGGGTTAAATTTAAATTTTTG
Found at i:360757 original size:11 final size:12
Alignment explanation
Indices: 360730--360760 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
360720 GTTATGTGGT
360730 TGATGTGGCAGC
1 TGATGTGGCAGC
360742 TGATGTGGCA-C
1 TGATGTGGCAGC
360753 TGATGTGG
1 TGATGTGG
360761 TGTTGATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.16, C:0.13, G:0.42, T:0.29
Consensus pattern (12 bp):
TGATGTGGCAGC
Found at i:360782 original size:22 final size:22
Alignment explanation
Indices: 360742--360793 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
360732 ATGTGGCAGC
* *
360742 TGATGTGGCACTGATGTGGTGT
1 TGATGTGGCACTGACGTGGCGT
* *
360764 TGATGTGGTAGTGACGTGGCGT
1 TGATGTGGCACTGACGTGGCGT
*
360786 TGACGTGG
1 TGATGTGG
360794 ACATGGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.13, C:0.10, G:0.44, T:0.33
Consensus pattern (22 bp):
TGATGTGGCACTGACGTGGCGT
Found at i:373770 original size:29 final size:29
Alignment explanation
Indices: 373725--373807 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 29
373715 AAAATGAAAA
* *
373725 TTTAGAAAGTTAAGGGGTCAAAATATAACT
1 TTTAGAAAGTT-TGGGGTCAAAATACAACT
* * * *
373755 TTTAGAGAGTTTGGGGATTAAAATGCAATT
1 TTTAGAAAGTTTGGGG-TCAAAATACAACT
*
373785 TTTAGAAAGTTTGGAGTCTAAAA
1 TTTAGAAAGTTTGGGGTC-AAAA
373808 AGTAATTTTC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
29 5 0.12
30 37 0.88
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (29 bp):
TTTAGAAAGTTTGGGGTCAAAATACAACT
Found at i:373807 original size:30 final size:30
Alignment explanation
Indices: 373754--373816 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
373744 AAAATATAAC
* * *
373754 TTTTAGAGAGTTTGGGGATTAAAATGCAAT
1 TTTTAGAAAGTTTGGAGATTAAAAAGCAAT
*
373784 TTTTAGAAAGTTTGGAG-TCTAAAAAGTAAT
1 TTTTAGAAAGTTTGGAGAT-TAAAAAGCAAT
373814 TTT
1 TTT
373817 CAAGAAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (30 bp):
TTTTAGAAAGTTTGGAGATTAAAAAGCAAT
Found at i:374029 original size:9 final size:9
Alignment explanation
Indices: 374015--374039 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
374005 ATTATCGGAC
374015 AAATTAAAA
1 AAATTAAAA
374024 AAATTAAAA
1 AAATTAAAA
374033 AAATTAA
1 AAATTAA
374040 TTCAAGGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATTAAAA
Found at i:379399 original size:18 final size:18
Alignment explanation
Indices: 379376--379413 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
379366 GTGTTATGTT
379376 TAAGAGCCCTCTAGGTGA
1 TAAGAGCCCTCTAGGTGA
379394 TAAGAGCCCTCTAGGTGA
1 TAAGAGCCCTCTAGGTGA
379412 TA
1 TA
379414 GTGTAGTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (18 bp):
TAAGAGCCCTCTAGGTGA
Found at i:384507 original size:24 final size:24
Alignment explanation
Indices: 384479--384525 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
384469 TTCGTAAGTC
*
384479 AAATAAATTATGCTAATAAATACA
1 AAATAAATTATACTAATAAATACA
*
384503 AAATACATTATACTAATAAATAC
1 AAATAAATTATACTAATAAATAC
384526 TATATCTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Done.