Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009620.1 Kokia drynarioides strain JFW-HI SEQ_124336, 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: 106133
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:207 original size:10 final size:11
Alignment explanation
Indices: 180--208 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
170 GTGTCAGGTA
180 TATTTTTCTCG
1 TATTTTTCTCG
191 TATTTTTCTCG
1 TATTTTTCTCG
202 TATTTTT
1 TATTTTT
209 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (11 bp):
TATTTTTCTCG
Found at i:210 original size:13 final size:12
Alignment explanation
Indices: 177--209 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
167 TGGGTGTCAG
177 GTATATTTTTCTC
1 GTAT-TTTTTCTC
190 GTA-TTTTTCTC
1 GTATTTTTTCTC
201 GTATTTTTT
1 GTATTTTTT
210 TGAAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 5 0.26
13 3 0.16
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.67
Consensus pattern (12 bp):
GTATTTTTTCTC
Found at i:461 original size:32 final size:32
Alignment explanation
Indices: 421--491 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
411 TTATTAATTT
421 ATTTTTTTTGTATTATTTAAGTAAAAAATCCA
1 ATTTTTTTTGTATTATTTAAGTAAAAAATCCA
453 ATTTTTTTTGTATTATTTAAGTAAAAAATCCA
1 ATTTTTTTTGTATTATTTAAGTAAAAAATCCA
485 ATTTTTT
1 ATTTTTT
492 ACCTTAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (32 bp):
ATTTTTTTTGTATTATTTAAGTAAAAAATCCA
Found at i:10354 original size:19 final size:18
Alignment explanation
Indices: 10316--10354 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
10306 AAAATAAATA
* *
10316 AAATAATTTAATTATGTT
1 AAATAATTTAATAATATT
10334 AAATAATTTGAATAATATT
1 AAATAATTT-AATAATATT
10353 AA
1 AA
10355 TTTGAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
AAATAATTTAATAATATT
Found at i:10520 original size:29 final size:29
Alignment explanation
Indices: 10465--10520 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
10455 GAATTTGATG
* **
10465 CTCTATTATTTTAATTTTGTTGTTTTAGC
1 CTCTATTATTCTAATTTTGTTAATTTAGC
10494 CTCT-TTATTCTAATTTTTGTTAATTTA
1 CTCTATTATTCTAA-TTTTGTTAATTTA
10521 ATCTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.62
Consensus pattern (29 bp):
CTCTATTATTCTAATTTTGTTAATTTAGC
Found at i:14906 original size:25 final size:25
Alignment explanation
Indices: 14852--14906 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
14842 TAATATCATG
* *
14852 ATTAAATTATTATTTTATAAAATAA
1 ATTATATTATTATTTTATAAAAGAA
14877 ATTATATTATT-TTTTA-AAAGAGAA
1 ATTATATTATTATTTTATAAA-AGAA
14901 AGTTAT
1 A-TTAT
14907 TAATTTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 3 0.12
24 9 0.35
25 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (25 bp):
ATTATATTATTATTTTATAAAAGAA
Found at i:38376 original size:2 final size:2
Alignment explanation
Indices: 38365--38398 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
38355 TCTATACTTC
38365 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38399 TGGTGAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39107 original size:19 final size:19
Alignment explanation
Indices: 39065--39111 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
39055 TCATTGTCTA
39065 AATTTATTTTATAATTTCT
1 AATTTATTTTATAATTTCT
* *
39084 AATTTTTTTTATAATTTTT
1 AATTTATTTTATAATTTCT
*
39103 TATTTATTT
1 AATTTATTT
39112 AGAATGAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
AATTTATTTTATAATTTCT
Found at i:40103 original size:22 final size:20
Alignment explanation
Indices: 40073--40118 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
40063 AAACTAATGG
*
40073 TTTTATTTATTATTGCATTTAT
1 TTTTATTTATTAGT-C-TTTAT
*
40095 TTTTCTTTATTAGTCTTTAT
1 TTTTATTTATTAGTCTTTAT
40115 TTTT
1 TTTT
40119 GTTGTTGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 12 0.55
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (20 bp):
TTTTATTTATTAGTCTTTAT
Found at i:40533 original size:16 final size:16
Alignment explanation
Indices: 40501--40548 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
40491 TTATTACAGT
* *
40501 TCTATTTCATTAAAAC
1 TCTATTCCATTATAAC
* *
40517 TTTATTCCGTTATAAC
1 TCTATTCCATTATAAC
40533 TCTATTCCATTATAAC
1 TCTATTCCATTATAAC
40549 GAATCAAACG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.02, T:0.46
Consensus pattern (16 bp):
TCTATTCCATTATAAC
Found at i:41678 original size:25 final size:25
Alignment explanation
Indices: 41644--41694 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
41634 TCAAATATAC
41644 ATAATCCGTCATCCACTCAGGATTT
1 ATAATCCGTCATCCACTCAGGATTT
*
41669 ATAATCCGTCTTCCACTCAGGATTT
1 ATAATCCGTCATCCACTCAGGATTT
41694 A
1 A
41695 GGTATGTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (25 bp):
ATAATCCGTCATCCACTCAGGATTT
Found at i:57165 original size:35 final size:33
Alignment explanation
Indices: 57114--57186 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
57104 TTTACTAATA
*
57114 ATTTA-AATAATTTTTAATA-TATATGTATTTCAT
1 ATTTATAACAATTTTTAATATTATATG-ATTT-AT
57147 ATTTATAACAATTATTTAATATTATATGATTTAT
1 ATTTATAACAATT-TTTAATATTATATGATTTAT
*
57181 TTTTAT
1 ATTTAT
57187 TATTTATACC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 5 0.14
34 13 0.37
35 11 0.31
36 6 0.17
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (33 bp):
ATTTATAACAATTTTTAATATTATATGATTTAT
Found at i:65988 original size:12 final size:12
Alignment explanation
Indices: 65971--65998 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
65961 CAGTCATTAA
65971 TAGCATCAATAT
1 TAGCATCAATAT
65983 TAGCATCAATAT
1 TAGCATCAATAT
65995 TAGC
1 TAGC
65999 CACATAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (12 bp):
TAGCATCAATAT
Found at i:67953 original size:42 final size:43
Alignment explanation
Indices: 67856--67958 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 43
67846 ATTTTCATCC
* * * *
67856 CCATCCTTGCCCCACGA-CTCGTTGCAGGTACAAAACTCAAAA
1 CCATCCTCGCCCCACGACCTCGCTGCAAGTACAAAACACAAAA
* * *
67898 CCATCCCCTCCCCACGACCT-GCTGCAAGTATAAAACACAAAA
1 CCATCCTCGCCCCACGACCTCGCTGCAAGTACAAAACACAAAA
*
67940 CCATCCTCGCCCCATGACC
1 CCATCCTCGCCCCACGACC
67959 CGCAATACTA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 48 0.96
43 2 0.04
ACGTcount: A:0.30, C:0.42, G:0.12, T:0.17
Consensus pattern (43 bp):
CCATCCTCGCCCCACGACCTCGCTGCAAGTACAAAACACAAAA
Found at i:68445 original size:29 final size:29
Alignment explanation
Indices: 68412--68468 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
68402 ACTTAATCAC
*
68412 TTTAATATTAAATTAATATAATACTTATA
1 TTTAATATTAAATTAATAGAATACTTATA
*
68441 TTTAATATTAAATTAATAGAATAGTTAT
1 TTTAATATTAAATTAATAGAATACTTAT
68469 CTACAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (29 bp):
TTTAATATTAAATTAATAGAATACTTATA
Found at i:68457 original size:24 final size:24
Alignment explanation
Indices: 68397--68458 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 24
68387 TTCAACTATG
68397 ATTAAACTTAATCACTTTAATATTAA
1 ATTAAA-TTAAT-ACTTTAATATTAA
68423 ATT-AATATAATAC-TT-ATATTTAA
1 ATTAAAT-TAATACTTTAATA-TTAA
68446 TATTAAATTAATA
1 -ATTAAATTAATA
68459 GAATAGTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
22 3 0.09
23 6 0.19
24 11 0.34
25 9 0.28
26 3 0.09
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTAAATTAATACTTTAATATTAA
Found at i:78746 original size:20 final size:21
Alignment explanation
Indices: 78653--78749 Score: 112
Period size: 20 Copynumber: 4.8 Consensus size: 21
78643 TGTATATCCT
*
78653 GCACAAAGCCTG-TTACACCG
1 GCACAAAGCCTGAATACACCG
78673 GCACAAAGCCT-AATACACCG
1 GCACAAAGCCTGAATACACCG
* * *
78693 GCATAAAACCTG-ATACACTG
1 GCACAAAGCCTGAATACACCG
*
78713 GCACAAAGCTTGAAT-CACCG
1 GCACAAAGCCTGAATACACCG
*
78733 GCATAAAGCCTGAATAC
1 GCACAAAGCCTGAATAC
78750 TTAGGTACAA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 60 0.95
21 3 0.05
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.15
Consensus pattern (21 bp):
GCACAAAGCCTGAATACACCG
Found at i:85103 original size:20 final size:21
Alignment explanation
Indices: 85014--85106 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 21
85004 TATGCTGCAC
* *
85014 AAAGCCTG-TTACATCGACAT
1 AAAGCCTGAATACACCGACAT
*
85034 AAAGCCT-AATACACCGGCAT
1 AAAGCCTGAATACACCGACAT
* *
85054 AAAGCCTG-ATACACCGGCAC
1 AAAGCCTGAATACACCGACAT
85074 AAAGCCTGAAT-CACCGACAT
1 AAAGCCTGAATACACCGACAT
85094 AAAGCCTGAATAC
1 AAAGCCTGAATAC
85107 TTAGGTATAC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
20 60 0.95
21 3 0.05
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.16
Consensus pattern (21 bp):
AAAGCCTGAATACACCGACAT
Found at i:85619 original size:12 final size:13
Alignment explanation
Indices: 85599--85631 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
85589 ATCTTAGTAA
*
85599 ATATATGTA-TTT
1 ATATTTGTATTTT
85611 ATATTTGTATTTT
1 ATATTTGTATTTT
85624 ATATTTGT
1 ATATTTGT
85632 TGATACAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (13 bp):
ATATTTGTATTTT
Found at i:87500 original size:6 final size:6
Alignment explanation
Indices: 87489--87517 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
87479 AATATGCCAC
87489 CGTCAT CGTCAT CGTCAT CGTCAT CGTCA
1 CGTCAT CGTCAT CGTCAT CGTCAT CGTCA
87518 ACACCATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.31
Consensus pattern (6 bp):
CGTCAT
Found at i:88112 original size:88 final size:89
Alignment explanation
Indices: 87983--88163 Score: 346
Period size: 88 Copynumber: 2.0 Consensus size: 89
87973 TTTTCCCTAC
87983 AATATTCACTGAAAAACTCTACCTGAATCAACAATTTCTTCCATGATTCTGGGTCTTTTTTTTCA
1 AATATTCACTGAAAAACTCTACCTGAATCAACAATTTCTTCCATGATTCTGGGTCTTTTTTTTCA
88048 -TTTTTTTCCTATAAAAGGAAAAA
66 TTTTTTTTCCTATAAAAGGAAAAA
*
88071 AATATTCACTGAAAAACTCTACCTGATTCAACAATTTCTTCCATGATTCTGGGTCTTTTTTTTCA
1 AATATTCACTGAAAAACTCTACCTGAATCAACAATTTCTTCCATGATTCTGGGTCTTTTTTTTCA
88136 TTTTTTTTCCTATAAAAGGAAAAA
66 TTTTTTTTCCTATAAAAGGAAAAA
88160 AATA
1 AATA
88164 CTAGTAAGCA
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
88 64 0.70
89 27 0.30
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (89 bp):
AATATTCACTGAAAAACTCTACCTGAATCAACAATTTCTTCCATGATTCTGGGTCTTTTTTTTCA
TTTTTTTTCCTATAAAAGGAAAAA
Found at i:88953 original size:2 final size:2
Alignment explanation
Indices: 88946--88978 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
88936 TATTATAATC
88946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
88979 TATCATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90814 original size:21 final size:21
Alignment explanation
Indices: 90776--90815 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
90766 GAGCCGACAG
*
90776 TGCTTCTTCAGCTTTCTCCCT
1 TGCTTCTTCAGCTGTCTCCCT
90797 TGCTTCTTC-GCATGTCTCC
1 TGCTTCTTCAGC-TGTCTCC
90816 ATACCCGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.05, C:0.38, G:0.12, T:0.45
Consensus pattern (21 bp):
TGCTTCTTCAGCTGTCTCCCT
Found at i:93090 original size:31 final size:31
Alignment explanation
Indices: 93019--93086 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
93009 AGTCTGTGTA
*
93019 TTTTAATTTCATCAATTTTAGTCCACCTACC
1 TTTTAATTTCATCAATTTTAGTCCACATACC
*
93050 TTTTGAATTT-ATCAATTTTAGTCC-CTATACT
1 TTTT-AATTTCATCAATTTTAGTCCAC-ATACC
93081 TTTTAA
1 TTTTAA
93087 ATTTTGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 3 0.09
31 25 0.76
32 5 0.15
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.50
Consensus pattern (31 bp):
TTTTAATTTCATCAATTTTAGTCCACATACC
Found at i:97020 original size:15 final size:15
Alignment explanation
Indices: 96997--97030 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
96987 TACTATTAAG
*
96997 ATTTTTTTTATAAAT
1 ATTTATTTTATAAAT
*
97012 ATTTATTTTTTAAAT
1 ATTTATTTTATAAAT
97027 ATTT
1 ATTT
97031 TTATTATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTATTTTATAAAT
Found at i:99408 original size:50 final size:46
Alignment explanation
Indices: 99361--99471 Score: 91
Period size: 48 Copynumber: 2.2 Consensus size: 46
99351 CAAAAAATTA
* *
99361 TAAAAATAAAAAATAAGAATTATTAAATT-TTAATAAAAATATAAAAA-TA
1 TAAAAATAAAAAA-AA-AA-TA-TAAATTCATAA-AAAAAGATAAAAATTA
*
99410 TTAAAAATTAGAAAAAAAAATATAAATTCATAAAAAAAGATATAAAATCA
1 -TAAAAA-TA-AAAAAAAAATATAAATTCATAAAAAAAGATA-AAAATTA
99460 TAAAATATAAAA
1 TAAAA-ATAAAA
99472 TTTTAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
48 17 0.33
49 16 0.31
50 10 0.19
51 4 0.08
52 5 0.10
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (46 bp):
TAAAAATAAAAAAAAAATATAAATTCATAAAAAAAGATAAAAATTA
Found at i:99436 original size:19 final size:20
Alignment explanation
Indices: 99414--99455 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
99404 AAAATATTAA
99414 AAATT-AGAAAAAAAAATAT
1 AAATTCAGAAAAAAAAATAT
* *
99433 AAATTCATAAAAAAAGATAT
1 AAATTCAGAAAAAAAAATAT
99453 AAA
1 AAA
99456 ATCATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATTCAGAAAAAAAAATAT
Found at i:99444 original size:20 final size:20
Alignment explanation
Indices: 99421--99464 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
99411 TAAAAATTAG
*
99421 AAAAAAAAATATAAATTCAT
1 AAAAAAAAATATAAAATCAT
*
99441 AAAAAAAGATATAAAATCAT
1 AAAAAAAAATATAAAATCAT
99461 AAAA
1 AAAA
99465 TATAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAAAAAATATAAAATCAT
Found at i:99786 original size:17 final size:18
Alignment explanation
Indices: 99735--99840 Score: 83
Period size: 19 Copynumber: 5.8 Consensus size: 18
99725 TTTTAATGCA
99735 TTTTATAATTTTTTA-TGAT
1 TTTTATAA-TTTTTACT-AT
*
99754 TTTTATAAAATTTTACTAT
1 TTTTAT-AATTTTTACTAT
*
99773 TTTTAT-ATTTTTACAAT
1 TTTTATAATTTTTACTAT
*
99790 TTTAATAATTTTTA-TAT
1 TTTTATAATTTTTACTAT
** *
99807 TTTTATTAAAATTTAATAAT
1 TTTTA-TAATTTTTACT-AT
*
99827 TTTTATAACTTTTA
1 TTTTATAATTTTTA
99841 GTCATATGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
17 20 0.28
18 14 0.20
19 27 0.38
20 10 0.14
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTTATAATTTTTACTAT
Found at i:99812 original size:8 final size:8
Alignment explanation
Indices: 99744--99812 Score: 57
Period size: 9 Copynumber: 7.9 Consensus size: 8
99734 ATTTTATAAT
99744 TTTTTATGA
1 TTTTTAT-A
99753 TTTTTATAAA
1 TTTTTAT--A
*
99763 ATTTTACTA
1 TTTTTA-TA
99772 TTTTTATA
1 TTTTTATA
*
99780 TTTTTACAA
1 TTTTTA-TA
*
99789 TTTTAATAA
1 TTTTTAT-A
99798 TTTTTATA
1 TTTTTATA
99806 TTTTTAT
1 TTTTTAT
99813 TAAAATTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
8 16 0.33
9 26 0.53
10 6 0.12
11 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (8 bp):
TTTTTATA
Found at i:99830 original size:28 final size:27
Alignment explanation
Indices: 99734--99833 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 27
99724 TTTTTAATGC
*
99734 ATTTTATAATTTTTTATGATTTTTATAAA
1 ATTTAATAA-TTTTTAT-ATTTTTATAAA
* *
99763 ATTTTACT-ATTTTTATATTTTTA-CAA
1 A-TTTAATAATTTTTATATTTTTATAAA
*
99789 TTTTAATAATTTTTATATTTTTATTAAA
1 ATTTAATAATTTTTATATTTTTA-TAAA
99817 ATTTAATAATTTTTATA
1 ATTTAATAATTTTTATA
99834 ACTTTTAGTC
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.08
26 17 0.28
27 7 0.12
28 25 0.42
29 2 0.03
30 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (27 bp):
ATTTAATAATTTTTATATTTTTATAAA
Found at i:101763 original size:31 final size:32
Alignment explanation
Indices: 101708--101768 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
101698 AAAGTGATGT
*
101708 AATTTTTTGAATTTAAGAGACATAATTTTTTG
1 AATTTTTTGAATTCAAGAGACATAATTTTTTG
* *
101740 AATTTTTTGAA-TCAAGTGGCATAATTTTT
1 AATTTTTTGAATTCAAGAGACATAATTTTT
101769 GGTTACTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (32 bp):
AATTTTTTGAATTCAAGAGACATAATTTTTTG
Found at i:102302 original size:91 final size:91
Alignment explanation
Indices: 102137--102397 Score: 477
Period size: 91 Copynumber: 2.9 Consensus size: 91
102127 TTCCATTTTA
*
102137 ATAACCAAACACATTTTACATGACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTAT
1 ATAA-CAAACACATTTTACATAACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTAT
102202 TATAACTATGTGTTCGTAATCAAGTAT
65 TATAACTATGTGTTCGTAATCAAGTAT
*
102229 ATAACAAAAACATTTTACATAACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTATT
1 ATAACAAACACATTTTACATAACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTATT
102294 ATAACTATGTGTTCGTAATCAAGTAT
66 ATAACTATGTGTTCGTAATCAAGTAT
*
102320 ATAACAAACACATTTTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAAAGACACTATT
1 ATAACAAACACATTTTACATAACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTATT
*
102385 ATGACTATGTGTT
66 ATAACTATGTGTT
102398 ACTTACATAA
Statistics
Matches: 164, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 160 0.98
92 4 0.02
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (91 bp):
ATAACAAACACATTTTACATAACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTATT
ATAACTATGTGTTCGTAATCAAGTAT
Found at i:102440 original size:66 final size:66
Alignment explanation
Indices: 102334--102463 Score: 251
Period size: 66 Copynumber: 2.0 Consensus size: 66
102324 CAAACACATT
102334 TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAAAGACACTATTATGACTATGTGTTA
1 TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAAAGACACTATTATGACTATGTGTTA
102399 C
66 C
*
102400 TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAACGACACTATTATGACTATGTGTT
1 TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAAAGACACTATTATGACTATGTGTT
102464 CGTAATCAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (66 bp):
TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAAAGACACTATTATGACTATGTGTTA
C
Found at i:102529 original size:157 final size:157
Alignment explanation
Indices: 102243--102554 Score: 588
Period size: 157 Copynumber: 2.0 Consensus size: 157
102233 CAAAAACATT
102243 TTACATAACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTATTATAACTATGTGTTC
1 TTACATAACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTATTATAACTATGTGTTC
102308 GTAATCAAGTATATAACAAACACATTTTACATAACAATTTCAACATCAGTCAATGCCCAATATCC
66 GTAATCAAGTATATAACAAACACATTTTACATAACAATTTCAACATCAGTCAATGCCCAATATCC
102373 AAAGACACTATTATGACTATGTGTTAC
131 AAAGACACTATTATGACTATGTGTTAC
* * *
102400 TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAACGACACTATTATGACTATGTGTTC
1 TTACATAACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTATTATAACTATGTGTTC
102465 GTAATCAAGTATATAACAAACACATTTTACATAACAATTTCAACATCAGTCAATGCCCAATATCC
66 GTAATCAAGTATATAACAAACACATTTTACATAACAATTTCAACATCAGTCAATGCCCAATATCC
*
102530 AACGACACTATTATGACTATGTGTT
131 AAAGACACTATTATGACTATGTGTT
102555 TGTAATCAAG
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 151 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (157 bp):
TTACATAACAATTTCAACATCAGTCAATGCACAATATCCAAAGACACTATTATAACTATGTGTTC
GTAATCAAGTATATAACAAACACATTTTACATAACAATTTCAACATCAGTCAATGCCCAATATCC
AAAGACACTATTATGACTATGTGTTAC
Found at i:102560 original size:91 final size:91
Alignment explanation
Indices: 102400--102566 Score: 325
Period size: 91 Copynumber: 1.8 Consensus size: 91
102390 TATGTGTTAC
102400 TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAACGACACTATTATGACTATGTGTTC
1 TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAACGACACTATTATGACTATGTGTTC
102465 GTAATCAAGTATATAACAAACACATT
66 GTAATCAAGTATATAACAAACACATT
*
102491 TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAACGACACTATTATGACTATGTGTTT
1 TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAACGACACTATTATGACTATGTGTTC
102556 GTAATCAAGTA
66 GTAATCAAGTA
102567 ATTAATTTTA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.31
Consensus pattern (91 bp):
TTACATAACAATTTCAACATCAGTCAATGCCCAATATCCAACGACACTATTATGACTATGTGTTC
GTAATCAAGTATATAACAAACACATT
Found at i:104779 original size:59 final size:59
Alignment explanation
Indices: 104739--105446 Score: 740
Period size: 59 Copynumber: 12.0 Consensus size: 59
104729 TTTTGAGAGT
** * * *
104739 TTCGAGGTCGAAAATGGGATTTTTGGAAGTTCATAAGTAAATTGGTAATTTTTGGAATG
1 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTCATAGGTAAAATGGTAATTTTTGGAAGG
* * ** *
104798 TTCGGGGTCAAAAATTAGATTTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTGGAAGG
1 TTCGAGGTTAAAAATGGGA-TTTTTGGAAGTTC-ATAGGTAAAATGGTAATTTTTGGAAGG
* * * *
104858 TTCGGGGTTAAAAATGGGA-TTTTAGAAGTTCGA-GGGTAAAATGATAATTTTTGGAAGG
1 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTC-ATAGGTAAAATGGTAATTTTTGGAAGG
104916 TTCG-GGTTAAAAATGGGATTTTTGGAAGTT--TGAGGGTAAAATGGTAATTTTTGGAAGG
1 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTCAT-A-GGTAAAATGGTAATTTTTGGAAGG
* * **
104974 TTCAAGGTTAAAAATGTGATTTTTGGAAGTTCAGGGGTAAAAATGGTAATTTTTGGAAGG
1 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTCATAGGT-AAAATGGTAATTTTTGGAAGG
105034 TTCGAGGTTAAAAATGGGATTTTTGGAAGTT--TGAGGGTAAAATGGTAATTTTTGGAAGG
1 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTCAT-A-GGTAAAATGGTAATTTTTGGAAGG
* * ** *
105093 TTCAAGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAGAATGGTAATTTTTGGAAGG
1 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTCATAGGTAAAATGGTAATTTTTGGAAGG
* * ** * *
105152 TT-TAGGGTTAAAAATGGGATTTTTGAAAGTTCAGGGGTAAAATGGTAATTTTCGAAAGG
1 TTCGA-GGTTAAAAATGGGATTTTTGGAAGTTCATAGGTAAAATGGTAATTTTTGGAAGG
* * * * * * *
105211 TTCG-GGGTCAAAATAGGATTTTTGTAAGTTCGA-GGGTAAAATGGTAA-TTTAGGAATG
1 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTC-ATAGGTAAAATGGTAATTTTTGGAAGG
* ***
105268 TTC-AGGGTTAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGG
1 TTCGA-GGTTAAAAATGGGATTTTTGGAAGTTCATAGGTAAAATGGTAATTTTTGGAAGG
* * * *** *
105327 TTCAAGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATCGTAATTTTTGGAAGG
1 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTCATAGGTAAAATGGTAATTTTTGGAAGG
* * *** * *
105386 TTCAAGGTTAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATTGTATTTTTTGGAAGG
1 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTCATAGGTAAAATGGTAATTTTTGGAAGG
105445 TT
1 TT
105447 TAGGGATCTT
Statistics
Matches: 572, Mismatches: 55, Indels: 44
0.85 0.08 0.07
Matches are distributed among these distances:
57 24 0.04
58 151 0.26
59 292 0.51
60 104 0.18
61 1 0.00
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (59 bp):
TTCGAGGTTAAAAATGGGATTTTTGGAAGTTCATAGGTAAAATGGTAATTTTTGGAAGG
Found at i:104824 original size:31 final size:28
Alignment explanation
Indices: 104783--105443 Score: 445
Period size: 29 Copynumber: 22.5 Consensus size: 28
104773 AAGTAAATTG
104783 GTAATTTTTGGAATGTTCGGGGTCAAAAAT
1 GTAATTTTTGGAA-GTTCGGGGT-AAAAAT
104813 -TAGATTTTTTGGAAGTTCGAGGGT-AAAAT
1 GTA-A-TTTTTGGAAGTTCG-GGGTAAAAAT
104842 GGTAATTTTTGGAAGGTTCGGGGTTAAAAAT
1 -GTAATTTTTGGAA-GTTCGGGG-TAAAAAT
** *
104873 GGGA-TTTTAGAAGTTCGAGGGT-AAAAT
1 GTAATTTTTGGAAGTTCG-GGGTAAAAAT
*
104900 GATAATTTTTGGAAGGTTCGGGTTAAAAAT
1 G-TAATTTTTGGAA-GTTCGGGGTAAAAAT
** *
104930 GGGATTTTTGGAAGTTTGAGGGT-AAAAT
1 GTAATTTTTGGAAGTTCG-GGGTAAAAAT
* *
104958 GGTAATTTTTGGAAGGTTCAAGGTTAAAAAT
1 -GTAATTTTTGGAA-GTTC-GGGGTAAAAAT
*
104989 GTGATTTTTGGAAGTTCAGGGGTAAAAAT
1 GTAATTTTTGGAAGTTC-GGGGTAAAAAT
*
105018 GGTAATTTTTGGAAGGTTCGAGGTTAAAAAT
1 -GTAATTTTTGGAA-GTTCG-GGGTAAAAAT
** *
105049 GGGATTTTTGGAAGTTTGAGGGT-AAAAT
1 GTAATTTTTGGAAGTTCG-GGGTAAAAAT
* *
105077 GGTAATTTTTGGAAGGTTCAAGGTTAAAAAT
1 -GTAATTTTTGGAA-GTTC-GGGGTAAAAAT
** * *
105108 GGGATTTTTGGAAGTTTAGGGGT-AGAAT
1 GTAATTTTTGGAAG-TTCGGGGTAAAAAT
* *
105136 GGTAATTTTTGGAAGGTTTAGGGTTAAAAAT
1 -GTAATTTTTGGAA-G-TTCGGGGTAAAAAT
** *
105167 GGGATTTTTGAAAGTTCAGGGGT-AAAAT
1 GTAATTTTTGGAAGTTC-GGGGTAAAAAT
* * *
105195 GGTAATTTTCGAAAGGTTCGGGGTCAAAAT
1 -GTAATTTTTGGAA-GTTCGGGGTAAAAAT
* *
105225 AG-GATTTTTGTAAGTTCGAGGGT-AAAAT
1 -GTAATTTTTGGAAGTTCG-GGGTAAAAAT
* *
105253 GGTAA-TTTAGGAATGTTCAGGGTTAAAAAT
1 -GTAATTTTTGGAA-GTTC-GGGGTAAAAAT
105283 G-AGATTTTTGGAAGTTCGGGGGT-AAAAT
1 GTA-ATTTTTGGAAGTTC-GGGGTAAAAAT
**
105311 GGTAATTTTTGGAAGGTTCAAGGTCAAAAAT
1 -GTAATTTTTGGAA-GTTCGGGGT-AAAAAT
105342 G-AGATTTTTGGAAGTTCGGGGGT-AAAAT
1 GTA-ATTTTTGGAAGTTC-GGGGTAAAAAT
* *
105370 CGTAATTTTTGGAAGGTTCAAGGTTAAAAAT
1 -GTAATTTTTGGAA-GTTC-GGGGTAAAAAT
*
105401 G-AGATTTTTGGAAGTTCGGGGGTAAAATT
1 GTA-ATTTTTGGAAGTTC-GGGGTAAAAAT
*
105430 GTATTTTTTGGAAG
1 GTAATTTTTGGAAG
105444 GTTTAGGGAT
Statistics
Matches: 506, Mismatches: 72, Indels: 107
0.74 0.11 0.16
Matches are distributed among these distances:
27 6 0.01
28 60 0.12
29 215 0.42
30 168 0.33
31 57 0.11
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.35
Consensus pattern (28 bp):
GTAATTTTTGGAAGTTCGGGGTAAAAAT
Done.