Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005604.1 Kokia drynarioides strain JFW-HI SEQ_119742, 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: 40135
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Found at i:527 original size:22 final size:22
Alignment explanation
Indices: 486--528 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
476 ACATCTGTTT
*
486 ACATAACACTTGAAATTATATG
1 ACATAACACATGAAATTATATG
508 ACATAACACAT-AAATATATAT
1 ACATAACACATGAAAT-TATAT
529 TTAATGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (22 bp):
ACATAACACATGAAATTATATG
Found at i:10733 original size:52 final size:52
Alignment explanation
Indices: 10660--10950 Score: 433
Period size: 52 Copynumber: 5.6 Consensus size: 52
10650 ATTTCATTTA
* *
10660 ATACTCACGATGACACATAGTCATCAGACCTCACAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
*
10712 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* * *
10764 ATACTCAAGATGACA-AGTAGTCATTGGATCTCATAAT-TCGTAAAGGATTCAT
1 ATACTCACGATGACACA-TAGTCATCGGACCTCATAATCT-GTAAAGGATTCAT
* * *
10816 ATACTCACGATGACACATAATCATCGGACATCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* * *
10868 ATACTCACGATGACACATAGTCATCGGACATCATAATCCGTAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
*
10920 ATACTCACGATGACACATAATCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
10951 TTACATTTAA
Statistics
Matches: 218, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
51 2 0.01
52 215 0.99
53 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
Found at i:13747 original size:20 final size:21
Alignment explanation
Indices: 13713--13753 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
13703 TAGGCATTGA
*
13713 TTTTACAGAAGAATAATAATT
1 TTTTAAAGAAGAATAATAATT
13734 TTTTAAAGAA-AATAATAATT
1 TTTTAAAGAAGAATAATAATT
13754 AAAATCTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTAAAGAAGAATAATAATT
Found at i:13951 original size:26 final size:26
Alignment explanation
Indices: 13903--13971 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 26
13893 AATCCATAGA
**
13903 TATATAGATTATCTATTTTATTATTAT
1 TATATAGA-TATAGATTTTATTATTAT
13930 TATATAGATATAGATTTTATTATTAT
1 TATATAGATATAGATTTTATTATTAT
13956 TATATAGATATAGATT
1 TATATAGATATAGATT
13972 AATTATATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 32 0.80
27 8 0.20
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (26 bp):
TATATAGATATAGATTTTATTATTAT
Found at i:13960 original size:20 final size:22
Alignment explanation
Indices: 13923--13964 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
13913 ATCTATTTTA
13923 TTATTATTATATAGATATAGATT
1 TTATTATTATATA-ATATAGATT
13946 TTATTATTAT-T-ATATAGAT
1 TTATTATTATATAATATAGAT
13965 ATAGATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
TTATTATTATATAATATAGATT
Found at i:14194 original size:21 final size:19
Alignment explanation
Indices: 14150--14194 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
14140 CTTTGAATCA
*
14150 TAAACCTCAACTCAAACTT
1 TAAACCTCAACTCAAACCT
*
14169 TAAACCTCGAACCTCGAACCT
1 TAAACCTC-AA-CTCAAACCT
14190 TAAAC
1 TAAAC
14195 TTTAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 2 0.09
21 12 0.55
ACGTcount: A:0.40, C:0.33, G:0.04, T:0.22
Consensus pattern (19 bp):
TAAACCTCAACTCAAACCT
Found at i:14596 original size:14 final size:14
Alignment explanation
Indices: 14577--14624 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
14567 GCTAATTTTT
14577 ACCTTGAACTCTAA
1 ACCTTGAACTCTAA
*
14591 ACCTTGAA-TCTCA
1 ACCTTGAACTCTAA
*
14604 A-CTTGAACTTTAA
1 ACCTTGAACTCTAA
*
14617 ACTTTGAA
1 ACCTTGAA
14625 TCTCAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 13 0.46
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (14 bp):
ACCTTGAACTCTAA
Found at i:14617 original size:26 final size:26
Alignment explanation
Indices: 14579--14630 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
14569 TAATTTTTAC
14579 CTTGAACTCTAAACCTTGAATCTCAA
1 CTTGAACTCTAAACCTTGAATCTCAA
* *
14605 CTTGAACTTTAAACTTTGAATCTCAA
1 CTTGAACTCTAAACCTTGAATCTCAA
14631 ATTTTAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (26 bp):
CTTGAACTCTAAACCTTGAATCTCAA
Found at i:18321 original size:31 final size:31
Alignment explanation
Indices: 18253--18323 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
18243 TTAATATTTG
* * *
18253 GATGACTAAAATGAAAGTACCTTAAAAATTA
1 GATGACCAAAATGAAAATACCTTAAAAATCA
18284 -AGTGACCAAAATGAAAATATCC-TAAAAATCA
1 GA-TGACCAAAATGAAAATA-CCTTAAAAATCA
18315 GATGACCAA
1 GATGACCAA
18324 TTAGTTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 1 0.03
31 30 0.88
32 3 0.09
ACGTcount: A:0.52, C:0.14, G:0.13, T:0.21
Consensus pattern (31 bp):
GATGACCAAAATGAAAATACCTTAAAAATCA
Found at i:18794 original size:18 final size:19
Alignment explanation
Indices: 18751--18800 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
18741 TAATTTATTT
18751 TTTATTT-T-ATATTATAA
1 TTTATTTATAATATTATAA
18768 TATTA-TTATAATATT-TAA
1 T-TTATTTATAATATTATAA
*
18786 TTTATTTATATTATT
1 TTTATTTATAATATT
18801 CACAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 6 0.21
18 17 0.61
19 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTATAATATTATAA
Found at i:19526 original size:21 final size:20
Alignment explanation
Indices: 19501--19542 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
19491 ATTATTTTTC
19501 ATATAAAAACAAATTTTAAAA
1 ATAT-AAAACAAATTTTAAAA
*
19522 ATATAATACAAATTTTAAAA
1 ATATAAAACAAATTTTAAAA
19542 A
1 A
19543 ATACACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
ATATAAAACAAATTTTAAAA
Found at i:19758 original size:11 final size:11
Alignment explanation
Indices: 19742--19774 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
19732 ACGAAATGAT
19742 AACAAAACAA-
1 AACAAAACAAC
19752 AAGCAAAACAAC
1 AA-CAAAACAAC
19764 AACAAAACAAC
1 AACAAAACAAC
19775 GTGGAGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 17 0.81
12 2 0.10
ACGTcount: A:0.73, C:0.24, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAACAAC
Found at i:20735 original size:24 final size:24
Alignment explanation
Indices: 20719--20794 Score: 143
Period size: 24 Copynumber: 3.2 Consensus size: 24
20709 TAGCTCACAC
20719 GAGCCCAGAATGGTTAGCTCTTAA
1 GAGCCCAGAATGGTTAGCTCTTAA
20743 GAGCCCAGAATGGTTAGCTCTTAA
1 GAGCCCAGAATGGTTAGCTCTTAA
*
20767 GAGCCCAGAATGGTTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAA
20791 GAGC
1 GAGC
20795 TAGAATCAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (24 bp):
GAGCCCAGAATGGTTAGCTCTTAA
Found at i:22674 original size:24 final size:24
Alignment explanation
Indices: 22627--22674 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
22617 CCACAGGGTA
* *
22627 ATCTGAAGGTGGAACCGGAGGTGC
1 ATCTGAAGGTGGAACCGAAAGTGC
* *
22651 ATCTGAAGGTGTATCCGAAAGTGC
1 ATCTGAAGGTGGAACCGAAAGTGC
22675 GGGCTTGTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.35, T:0.21
Consensus pattern (24 bp):
ATCTGAAGGTGGAACCGAAAGTGC
Found at i:26241 original size:49 final size:49
Alignment explanation
Indices: 26186--26284 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
26176 AAAATCAAGT
26186 AAAACTTCATCTTCTTCATGAAGTTAGAATAAAAAACCCTAGTTGGAGG
1 AAAACTTCATCTTCTTCATGAAGTTAGAATAAAAAACCCTAGTTGGAGG
26235 AAAACTTCATCTTCTTCATGAAGTTAGAATAAAAAACCCTAGTTGGAGG
1 AAAACTTCATCTTCTTCATGAAGTTAGAATAAAAAACCCTAGTTGGAGG
26284 A
1 A
26285 GAAGAGACAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (49 bp):
AAAACTTCATCTTCTTCATGAAGTTAGAATAAAAAACCCTAGTTGGAGG
Found at i:28030 original size:42 final size:42
Alignment explanation
Indices: 27459--28023 Score: 772
Period size: 42 Copynumber: 13.4 Consensus size: 42
27449 GCTTAACTTG
* * **
27459 ATGTATAAATGGAAGACTCATGTCTCGGGACAAGCATGAGATT
1 ATGTTTAAA-GGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
27502 ATGTTTAAAGGAAGACTCATGTATCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
27544 ATGGTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
27586 ATGTTTAAAGGAAGACTCGTGACTCGTGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
27628 ATGTTTAAAGGAAGACTCGTGACTCGGGATGAACATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
** * *
27670 ATGTTTAAAAAAAAGACTCGTGTCTTGGGATGAGCATAAGATT
1 ATGTTT-AAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
27713 ATGTTTAAAGGAAGACTCGTGTCTCGAGATGAGCATTAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
27755 ATGTTTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
**
27797 ATGTTTAAAGGAAGACTCGTAACTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * * *
27839 ATGTTTAACGAAATAATCGTGTCTCGGGATGAGCATG-GACTT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA-TT
* **
27881 ATGTTTAAAGGAAGACTCATGTCTTAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * *
27923 ATGTTTGAAGGAAAACTCGTGACTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * * *
27965 ATGGTTAAAGGAAAACTTGTGTCTCAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
28007 ATGTTTAAAGGAAGACT
1 ATGTTTAAAGGAAGACT
28024 TATGTCTTAG
Statistics
Matches: 464, Mismatches: 55, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
41 2 0.00
42 416 0.90
43 46 0.10
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.28
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
Found at i:28059 original size:42 final size:41
Alignment explanation
Indices: 27459--28087 Score: 350
Period size: 42 Copynumber: 14.9 Consensus size: 41
27449 GCTTAACTTG
* * * * * *
27459 ATGTATAAATGGAAGACTCATGTCTCGGGACAAGCATGAGATT
1 ATGTTTAAA-GGAAGACTTATGTCTCAGTA-GAGCATAAGATT
* * * * *
27502 ATGTTTAAAGGAAGACTCATGTATCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCAGTA-GAGCATAAGATT
* * * * *
27544 ATGGTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCAGTA-GAGCATAAGATT
** * *
27586 ATGTTTAAAGGAAGACTCGTGACTC-GTGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCAGT-A-GAGCATAAGATT
** * * * * *
27628 ATGTTTAAAGGAAGACTCGTGACTCGGGATGAACATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCAGTA-GAGCATAAGATT
** ** ** *
27670 ATGTTTAAAAAAAAGACTCGTGTCTTGGGATGAGCATAAGATT
1 ATGTTT-AAAGGAAGACTTATGTCTCAGTA-GAGCATAAGATT
** *
27713 ATGTTTAAAGGAAGACTCGTGTCTCGAG-ATGAGCATTAGATT
1 ATGTTTAAAGGAAGACTTATGTCTC-AGTA-GAGCATAAGATT
* *
27755 ATGTTTAAAGGAAGACTCATGTCTCGAG-ATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTC-AGTA-GAGCATAAGATT
** ** * * *
27797 ATGTTTAAAGGAAGACTCGTAACTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCAGTA-GAGCATAAGATT
* * * * ** * * *
27839 ATGTTTAACGAAATAATCGTGTCTCGGGATGAGCAT-GGACTT
1 ATGTTTAAAGGAAGACTTATGTCTCAGTA-GAGCATAAGA-TT
* * * *
27881 ATGTTTAAAGGAAGACTCATGTCTTAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCAGTA-GAGCATAAGATT
* * ** * * * *
27923 ATGTTTGAAGGAAAACTCGTGACTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCAGTA-GAGCATAAGATT
* * * * *
27965 ATGGTTAAAGGAAAACTTGTGTCTCAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCAGTA-GAGCATAAGATT
*
28007 ATGTTTAAAGGAAGACTTATGTCTTAGTAGAGCATAAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCAGTAGAGCATAAGATT
* *
28048 -TGTTTAAAAAGGAAGACTTATGACTCGGTTAGAGCATAAG
1 ATGTTT--AAAGGAAGACTTATGTCTCAG-TAGAGCATAAG
28088 GTTAATTCAG
Statistics
Matches: 512, Mismatches: 64, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
40 5 0.01
41 15 0.03
42 433 0.85
43 59 0.12
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (41 bp):
ATGTTTAAAGGAAGACTTATGTCTCAGTAGAGCATAAGATT
Found at i:29503 original size:145 final size:146
Alignment explanation
Indices: 29239--29530 Score: 543
Period size: 145 Copynumber: 2.0 Consensus size: 146
29229 ACAACCCGTT
* *
29239 TTTCAGTGGTGTCGAAAACAGTGATTTCGAGATCACAAACTCGACAAGAAAATTTTTATATTGAG
1 TTTCAGTGGTGTCGAAAACAATGATTTCGAGATCACAAACTCGACAAGAAAATTTTTATATTAAG
29304 TGATTAAATTAAATAAGTCAATATTAATTTTATATGGAATTTTGGATTGAGGAATTTTAATTATT
66 TGATTAAATTAAATAAGTCAATATTAATTTTATATGGAATTTTGGATTGAGGAATTTTAATTATT
29369 GAATTAAAAGTTAGTA
131 GAATTAAAAGTTAGTA
29385 TTTCAGTGGTGTCGAAAACAATGATTTCGAGATCACAAAC-CTGACAAGAAAA-TTTTATATTAA
1 TTTCAGTGGTGTCGAAAACAATGATTTCGAGATCACAAACTC-GACAAGAAAATTTTTATATTAA
29448 GTGATTAAATTAAATAAGTCAATATTAATTTTATATGGAATTTTGGATTGAGGAATTTTAATTAT
65 GTGATTAAATTAAATAAGTCAATATTAATTTTATATGGAATTTTGGATTGAGGAATTTTAATTAT
29513 TGAATTAAAAGTTAGTA
130 TGAATTAAAAGTTAGTA
29530 T
1 T
29531 AAGTGGTTTG
Statistics
Matches: 143, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
145 94 0.66
146 49 0.34
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (146 bp):
TTTCAGTGGTGTCGAAAACAATGATTTCGAGATCACAAACTCGACAAGAAAATTTTTATATTAAG
TGATTAAATTAAATAAGTCAATATTAATTTTATATGGAATTTTGGATTGAGGAATTTTAATTATT
GAATTAAAAGTTAGTA
Found at i:30951 original size:10 final size:10
Alignment explanation
Indices: 30938--30982 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
30928 TGTTTTATTT
30938 TACATATATA
1 TACATATATA
30948 TACACT-TATA
1 TACA-TATATA
30958 TACATATATA
1 TACATATATA
*
30968 TACATAGATA
1 TACATATATA
30978 TACAT
1 TACAT
30983 TTTGATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 1 0.03
10 30 0.94
11 1 0.03
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (10 bp):
TACATATATA
Found at i:31853 original size:30 final size:30
Alignment explanation
Indices: 31819--31879 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
31809 ATTTTCTTTG
31819 AAAATCACATTTTGACTCCT-AAACTTTTTA
1 AAAATCACATTTTGAC-CCTCAAACTTTTTA
* *
31849 AAAATTACATTTTGACCCTCATACTTTTTA
1 AAAATCACATTTTGACCCTCAAACTTTTTA
31879 A
1 A
31880 CATTGCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATCACATTTTGACCCTCAAACTTTTTA
Found at i:31938 original size:30 final size:30
Alignment explanation
Indices: 31849--31984 Score: 116
Period size: 30 Copynumber: 4.6 Consensus size: 30
31839 AAACTTTTTA
* * **
31849 AAAATTACATTTTGACCCTCATACTT-TTT
1 AAAATTACATTTTAACCCTCAAACTTATCC
* * * ** *
31878 AACATTGCATGTTAACCC-CAATTTTCTCC
1 AAAATTACATTTTAACCCTCAAACTTATCC
31907 AAAATTACATTTTAATCCCT-AAACTTATCC
1 AAAATTACATTTTAA-CCCTCAAACTTATCC
* *
31937 AAAATTACATTTTAACCCTCAAACTTTTCT
1 AAAATTACATTTTAACCCTCAAACTTATCC
* *
31967 AAAATTATATTTTGACCC
1 AAAATTACATTTTAACCC
31985 CATATCCTCC
Statistics
Matches: 84, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
28 4 0.05
29 31 0.37
30 49 0.58
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTCAAACTTATCC
Found at i:38459 original size:39 final size:39
Alignment explanation
Indices: 38411--38618 Score: 126
Period size: 39 Copynumber: 5.3 Consensus size: 39
38401 CAATCATTCG
* *
38411 ATCTTTTACCCCAAGCCTGGGATAGATCACCATAAGCCA
1 ATCTCTTACCCCAAGCCTGGGACAGATCACCATAAGCCA
* * **
38450 ATCTCTTACCCCGAGCCTAGGACAGATTGCAGCCATTTG---
1 ATCTCTTACCCCAAGCCTGGGACAGA-T-CA-CCATAAGCCA
* * * *
38489 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCAAGCCTGGGACAGATCACCATAAGCCA
* * *
38528 ATCTCTTATCCCAAGCCTAAGG-CAGATTGCAACCAT---CCG
1 ATCTCTTACCCCAAGCCT-GGGACAGA-T-C-ACCATAAGCCA
* * *
38567 ATCTTTTACCCCGAGCCTTAGGG-CAGATCACCATCAGCCA
1 ATCTCTTACCCCAAGCC-T-GGGACAGATCACCATAAGCCA
*
38607 ATTTCTTACCCC
1 ATCTCTTACCCC
38619 GAGCTTGAGG
Statistics
Matches: 132, Mismatches: 23, Indels: 27
0.73 0.13 0.15
Matches are distributed among these distances:
36 5 0.04
37 7 0.05
38 2 0.02
39 81 0.61
40 24 0.18
41 3 0.02
42 10 0.08
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCCCAAGCCTGGGACAGATCACCATAAGCCA
Found at i:38462 original size:78 final size:77
Alignment explanation
Indices: 38405--38830 Score: 442
Period size: 78 Copynumber: 5.4 Consensus size: 77
38395 AAATAACAAT
* *
38405 CATTCGATCTTTTACCCCAAGCCTGGGATAGATCACCATAAGCCAATCTCTTACCCCGAGCCT-A
1 CATTCGATCTTTTACCCCGAGCCTGGG-CAGATCACCATAAGCCAATCTCTTACCCCGAGCCTAA
*
38469 GGACAGATTGCAGC
65 GG-CAGATTGCAAC
* * * *
38483 CATTTGATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTATCCCAAGCCTAA
1 CATTCGATCTTTTACCCCGAGCCT-GGGCAGATCACCATAAGCCAATCTCTTACCCCGAGCCTAA
38548 GGCAGATTGCAAC
65 GGCAGATTGCAAC
* * * * *
38561 CATCCGATCTTTTACCCCGAGCCTTAGGGCAGATCACCATCAGCCAATTTCTTACCCCGAGCTTG
1 CATTCGATCTTTTACCCCGAGCC-T-GGGCAGATCACCATAAGCCAATCTCTTACCCCGAGCCTA
*
38626 AGGCAGATTGCAGC
64 AGGCAGATTGCAAC
* * * **
38640 CATTTGATCTTTTACCCCGAGCCTGAGGTAAATCACCATCAA-CCAATCTCTTACCCCGAGTTTA
1 CATTCGATCTTTTACCCCGAGCCTG-GGCAGATCACCAT-AAGCCAATCTCTTACCCCGAGCCTA
* ** * **
38704 GGGTTGGTTATAAC
64 AGGCAGATTGCAAC
* * * * * *
38718 CATTAGATCTTTTACCCTGAGCCTAAGACAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGA
1 CATTCGATCTTTTACCCCGAGCCT-GGGCAGATCACCATAAGCCAATCTCTTACCCCGAGCCTAA
* *
38783 GGCAGATTACAGC
65 GGCAGATTGCAAC
* * *
38796 CATCCGATCTTTTACCCCGATCATAGGGCAGATCA
1 CATTCGATCTTTTACCCCGAGCCT-GGGCAGATCA
38831 AGGTCAACCA
Statistics
Matches: 287, Mismatches: 54, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
77 2 0.01
78 209 0.73
79 76 0.26
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (77 bp):
CATTCGATCTTTTACCCCGAGCCTGGGCAGATCACCATAAGCCAATCTCTTACCCCGAGCCTAAG
GCAGATTGCAAC
Found at i:38655 original size:39 final size:38
Alignment explanation
Indices: 38450--38815 Score: 187
Period size: 39 Copynumber: 9.4 Consensus size: 38
38440 CCATAAGCCA
* **
38450 ATCTCTTACCCCGAGCCT-AGGACAGATTGCAGCCATTTG
1 ATCTTTTACCCCGAGCCTGAGG-CAGATTGCA-CCATCAG
*
38489 ATCTTTTACCCCGAGCCTGGGGCAGA-T-CACCATCAG
1 ATCTTTTACCCCGAGCCTGAGGCAGATTGCACCATCAG
* * * * *
38525 CCAATCTCTTATCCCAAGCCTAAGGCAGATTGCAACCATCCG
1 ---ATCTTTTACCCCGAGCCTGAGGCAGATTGC-ACCATCAG
*
38567 ATCTTTTACCCCGAGCCTTAGGGCAGA-T-CACCATCAG
1 ATCTTTTACCCCGAGCCTGA-GGCAGATTGCACCATCAG
* **
38604 CCAAT-TTCTTACCCCGAGCTTGAGGCAGATTGCAGCCATTTG
1 ---ATCTT-TTACCCCGAGCCTGAGGCAGATTGCA-CCATCAG
* * *
38646 ATCTTTTACCCCGAGCCTGAGGTA-AAT-CACCATCAACCA
1 ATCTTTTACCCCGAGCCTGAGGCAGATTGCACCATC-A--G
* * * ** * ** *
38685 ATCTCTTACCCCGAG-TTTAGGGTTGGTTATAACCATTAG
1 ATCTTTTACCCCGAGCCTGA-GGCAGATT-GCACCATCAG
* * *
38724 ATCTTTTACCCTGAGCCTAAGACAGA-T-CACCATCAG
1 ATCTTTTACCCCGAGCCTGAGGCAGATTGCACCATCAG
* * *
38760 CCAATCTCTTACCCCGAGCCTGAGGCAGATTACAGCCATCCG
1 ---ATCTTTTACCCCGAGCCTGAGGCAGATTGCA-CCATCAG
38802 ATCTTTTACCCCGA
1 ATCTTTTACCCCGA
38816 TCATAGGGCA
Statistics
Matches: 247, Mismatches: 50, Indels: 60
0.69 0.14 0.17
Matches are distributed among these distances:
36 16 0.06
37 11 0.04
38 7 0.03
39 153 0.62
40 31 0.13
41 6 0.02
42 23 0.09
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (38 bp):
ATCTTTTACCCCGAGCCTGAGGCAGATTGCACCATCAG
Found at i:38788 original size:235 final size:234
Alignment explanation
Indices: 38405--38830 Score: 595
Period size: 235 Copynumber: 1.8 Consensus size: 234
38395 AAATAACAAT
*
38405 CATTCGATCTTTTACCCCAAGCCTGGGATAGATCACCATAAGCCAATCTCTTACCCCGAGCCTAG
1 CATTCGATCTTTTACCCCAAGCCTGGGATAAATCACCATAAGCCAATCTCTTACCCCGAGCCTAG
* * * ** *
38470 GACAGATTGCAGCCATTTGATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTT
66 GACAGATTACAACCATTAGATCTTTTACCCCGAGCCTAAGACAGATCACCATCAGCCAATCTCTT
* * *
38535 ATCCCAAGCCTAAGGCAGATTGCAACCATCCGATCTTTTACCCCGAGCCTTAGGGCAGATCACCA
131 ACCCCAAGCCTAAGGCAGATTACAACCATCCGATCTTTTACCCCGA-CCATAGGGCAGATCACCA
38600 TCAGCCAATTTCTTACCCCGAGCTTGAGGCAGATTGCAGC
195 TCAGCCAATTTCTTACCCCGAGCTTGAGGCAGATTGCAGC
* * **
38640 CATTTGATCTTTTACCCCGAGCCTGAGG-TAAATCACCATCAA-CCAATCTCTTACCCCGAGTTT
1 CATTCGATCTTTTACCCCAAGCCTG-GGATAAATCACCAT-AAGCCAATCTCTTACCCCGAGCCT
*** * * *
38703 AGGGTTGGTTATAACCATTAGATCTTTTACCCTGAGCCTAAGACAGATCACCATCAGCCAATCTC
64 AGGACAGATTACAACCATTAGATCTTTTACCCCGAGCCTAAGACAGATCACCATCAGCCAATCTC
* * * *
38768 TTACCCCGAGCCTGAGGCAGATTACAGCCATCCGATCTTTTACCCCGATCATAGGGCAGATCA
129 TTACCCCAAGCCTAAGGCAGATTACAACCATCCGATCTTTTACCCCGACCATAGGGCAGATCA
38831 AGGTCAACCA
Statistics
Matches: 165, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
234 13 0.08
235 148 0.90
236 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (234 bp):
CATTCGATCTTTTACCCCAAGCCTGGGATAAATCACCATAAGCCAATCTCTTACCCCGAGCCTAG
GACAGATTACAACCATTAGATCTTTTACCCCGAGCCTAAGACAGATCACCATCAGCCAATCTCTT
ACCCCAAGCCTAAGGCAGATTACAACCATCCGATCTTTTACCCCGACCATAGGGCAGATCACCAT
CAGCCAATTTCTTACCCCGAGCTTGAGGCAGATTGCAGC
Found at i:38826 original size:39 final size:39
Alignment explanation
Indices: 38763--38984 Score: 121
Period size: 39 Copynumber: 5.7 Consensus size: 39
38753 CCATCAGCCA
* * *
38763 ATCTCTTACCCCGAGCCT-GAGGCAGATTACAGCCATCCG
1 ATCTCTTACCCCGATCATAG-GGCAGATCACAGCCATCCG
* * * *
38802 ATCTTTTACCCCGATCATAGGGCAGATCA-AGGTCAACCA
1 ATCTCTTACCCCGATCATAGGGCAGATCACA-GCCATCCG
* * *** * *
38841 ATCTCTTACTCTACGAT-A-AGGGAAGATTGTAACCATCTG
1 ATCTCTTAC-C-CCGATCATAGGGCAGATCACAGCCATCCG
* * * *
38880 ATCTTTTACACCGATCATGGGGCAGATCACAGTCATCCG
1 ATCTCTTACCCCGATCATAGGGCAGATCACAGCCATCCG
** * * * *
38919 ATCTCTTACCTTGACCAT-GAGGTAAATCACAGCCATCCA
1 ATCTCTTACCCCGATCATAG-GGCAGATCACAGCCATCCG
* * *
38958 ATCTCTTACCTCAATCATGGGGCAGAT
1 ATCTCTTACCCCGATCATAGGGCAGAT
38985 TGCAGTTATC
Statistics
Matches: 132, Mismatches: 42, Indels: 18
0.69 0.22 0.09
Matches are distributed among these distances:
37 4 0.03
38 3 0.02
39 116 0.88
40 5 0.04
41 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGATCATAGGGCAGATCACAGCCATCCG
Found at i:38868 original size:78 final size:79
Alignment explanation
Indices: 38473--38984 Score: 208
Period size: 78 Copynumber: 6.5 Consensus size: 79
38463 AGCCTAGGAC
* ** * * *
38473 AGATTGCAGCCATTTGATCTTTTACCCCGAGCCTGGGGCAGATCACCA-TCAGCCAATCTCTTAT
1 AGATTACAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCA-CAGTCAACCAATCTCTTA-
** *
38537 CC-CAAGCC-TAA-GGC
64 CCTTGA-CCATAAGGGA
* * * * * * *
38551 AGATTGCAACCATCCGATCTTTTACCCCGAGCCTTAGGGCAGATCACCA-TCAGCCAATTTCTTA
1 AGATTACAGCCATCCGATCTTTTACCCCGA-TCATGGGGCAGATCA-CAGTCAACCAATCTCTTA
** * * * *
38615 CCCCGAGCTTGA-GGC
64 CCTTGACCATAAGGGA
* ** * * * * *
38630 AGATTGCAGCCATTTGATCTTTTACCCCGAGCCTGAGGTAAATCACCA-TCAACCAATCTCTTAC
1 AGATTACAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCA-CAGTCAACCAATCTCTTAC
** ** * *
38694 CCCGA-GTTTAGGGT
65 CTTGACCATAAGGGA
* * * * ** * * * ** * *
38708 TGGTTATAACCATTAGATCTTTTACCCTGAGCCTAAGACAGATCACCA-TCAGCCAATCTCTTAC
1 AGATTACAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCA-CAGTCAACCAATCTCTTAC
** * *
38772 CCCGAGCC-TGA-GGC
65 CTTGA-CCATAAGGGA
*
38786 AGATTACAGCCATCCGATCTTTTACCCCGATCATAGGGCAGATCA-AGGTCAACCAATCTCTTA-
1 AGATTACAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCACA-GTCAACCAATCTCTTAC
*
38849 CTCT-ACGATAAGGGA
65 CT-TGACCATAAGGGA
** * * * * *
38864 AGATTGTAACCATCTGATCTTTTACACCGATCATGGGGCAGATCACAGTCATCCGATCTCTTACC
1 AGATTACAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCACAGTCAACCAATCTCTTACC
* *
38929 TTGACCATGAGGTA
66 TTGACCATAAGGGA
* * * * *
38943 A-ATCACAGCCATCCAATCTCTTACCTCAATCATGGGGCAGAT
1 AGATTACAGCCATCCGATCTTTTACCCCGATCATGGGGCAGAT
38985 TGCAGTTATC
Statistics
Matches: 343, Mismatches: 77, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
76 2 0.01
77 7 0.02
78 257 0.75
79 77 0.22
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (79 bp):
AGATTACAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCACAGTCAACCAATCTCTTACC
TTGACCATAAGGGA
Found at i:38906 original size:156 final size:154
Alignment explanation
Indices: 38434--38984 Score: 486
Period size: 156 Copynumber: 3.5 Consensus size: 154
38424 AGCCTGGGAT
* * **
38434 AGATCACCATAAGCCAATCTCTTACCCCGAGCCT-AGGACAGATTGCAGCCATTTGATCTTTTAC
1 AGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGG-CAGATTACAGCCATCCGATCTTTTAC
* * * * * * *
38498 CCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTATCCCAAGCCTAA-GGCAGATTGCAACC
65 CCCGAGCATGGGGCAGATCACCATCAACCAATCTCTTA-CTCACG-ATAAGGGAAGATTGTAACC
* *
38562 ATCCGATCTTTTACCCCGAGCCTTAGGGC
128 ATCTGATCTTTTA-CCCGA-CCATAGGGC
* * * **
38591 AGATCACCATCAGCCAATTTCTTACCCCGAGCTTGAGGCAGATTGCAGCCATTTGATCTTTTACC
1 AGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATTACAGCCATCCGATCTTTTACC
* * * * * * ** * *
38656 CCGAGCCTGAGGTAAATCACCATCAACCAATCTCTTAC-CCCGAGTTTAGGGTTGGTTATAACCA
66 CCGAGCATGGGGCAGATCACCATCAACCAATCTCTTACTCACGA--TAAGGGAAGATTGTAACCA
* *
38720 T-TAGATCTTTTACCCTGAGCC-TAAGAC
129 TCT-GATCTTTTACCC-GA-CCATAGGGC
38747 AGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATTACAGCCATCCGATCTTTTACC
1 AGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATTACAGCCATCCGATCTTTTACC
* * ***
38812 CCGATCATAGGGCAGATCAAGGTCAACCAATCTCTTACTCTACGATAAGGGAAGATTGTAACCAT
66 CCGAGCATGGGGCAGATCACCATCAACCAATCTCTTACTC-ACGATAAGGGAAGATTGTAACCAT
* *
38877 CTGATCTTTTACACCGATCATGGGGC
130 CTGATCTTTTAC-CCGACCATAGGGC
* * ** * * * * *
38903 AGATCA-CAGTCATCCGATCTCTTACCTTGA-CCATGAGGTAAATCACAGCCATCCAATCTCTTA
1 AGATCACCA-TCAGCCAATCTCTTACCCCGAGCC-TGAGGCAGATTACAGCCATCCGATCTTTTA
* * *
38966 CCTCAATCATGGGGCAGAT
64 CCCCGAGCATGGGGCAGAT
38985 TGCAGTTATC
Statistics
Matches: 326, Mismatches: 55, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
155 7 0.02
156 193 0.59
157 120 0.37
158 6 0.02
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (154 bp):
AGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATTACAGCCATCCGATCTTTTACC
CCGAGCATGGGGCAGATCACCATCAACCAATCTCTTACTCACGATAAGGGAAGATTGTAACCATC
TGATCTTTTACCCGACCATAGGGC
Found at i:40113 original size:2 final size:2
Alignment explanation
Indices: 40106--40135 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40096 TACATCCTTT
40106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
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):
TA
Done.