Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003370.1 Kokia drynarioides strain JFW-HI SEQ_116097, 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: 158552
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 258 characters in sequence are not A, C, G, or T
Found at i:20153 original size:2 final size:2
Alignment explanation
Indices: 20141--20180 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
20131 TTGCCGCGAG
20141 TA TA TA T- 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 TA TA TA TA T
20181 TCCTGCAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21619 original size:62 final size:60
Alignment explanation
Indices: 21540--22060 Score: 566
Period size: 61 Copynumber: 8.5 Consensus size: 60
21530 TGTTGGTCCC
* * *
21540 TTTTTCAAAT-AAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCAATGCCCGACACCTCCT
1 TTTTTCAGATAAAAAAATTTC-AAATTTTTTTGTGTTGGCCATGCAATGGCCGACACC-CCT
*** * * * *
21601 TTTTTTTTATAAAAAAATTTCAATTTTTTTTGTTGTTGGTCATGTAATGGCCAACACTCCC-
1 TTTTTCAGATAAAAAAATTTCAAATTTTTTTG-TGTTGGCCATGCAATGGCCGACAC-CCCT
*
21662 TTTTTCAGATAAAAAAATTTCAAAATTTTTTAGTGTTGGCCATGCAATGGCCGACACCCCCT
1 TTTTTCAGATAAAAAAATTTC-AAATTTTTTTGTGTTGGCCATGCAATGGCCGACA-CCCCT
* * * *
21724 GTTCTCAGATAAAAAAATTTTAAATTTTTTTGGTGTTGGTCATGCAATGGCCGACACCCCCT
1 TTTTTCAGATAAAAAAATTTCAAATTTTTTT-GTGTTGGCCATGCAATGGCCGACA-CCCCT
* * * * * *
21786 GTTCTCGGATAAAAAAAATTCAAATTTTTTTGTGTAGGCCATGCAATGGCCGACACCCCC
1 TTTTTCAGATAAAAAAATTTCAAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCT
* * * * **
21846 TTTTTCAAATAAAAAAAATTTCAAATTTTTTTAGTTTTAGCCATGTAATGGTTGACACCCCCT
1 TTTTTCAGAT-AAAAAAATTTCAAATTTTTTT-GTGTTGGCCATGCAATGGCCGACA-CCCCT
* * *
21909 TTTTT-AGATAAAAAATTTTCAAATTTTTTTAGTGTTGGTCATGCAATGGCCGACATACCC-
1 TTTTTCAGATAAAAAAATTTCAAATTTTTTT-GTGTTGGCCATGCAATGGCCGACA-CCCCT
* *
21969 -TTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATTGCCGACACCCCT
1 TTTTTCAGATAAAAAAATTTC-AAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCT
* *
22029 TTTTCTCGGATAAAAAATTTTCAAATTTTTTT
1 TTTT-TCAGATAAAAAAATTTCAAATTTTTTT
22061 NNNNNNNNNN
Statistics
Matches: 389, Mismatches: 56, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
59 7 0.02
60 46 0.12
61 172 0.44
62 154 0.40
63 10 0.03
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (60 bp):
TTTTTCAGATAAAAAAATTTCAAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCT
Found at i:21698 original size:123 final size:123
Alignment explanation
Indices: 21537--22060 Score: 592
Period size: 123 Copynumber: 4.3 Consensus size: 123
21527 GGGTGTTGGT
* * * *
21537 CCCTTTTTCAAAT-AAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCAATGCCCGACACCTCCT
1 CCCTTTTTCAGATAAAAAAATTTCAAAATTTTTTAGTGTTGGCCATGCAATGGCCGACACCTCCT
*** * * * * * *
21601 TTTTTTTTATAAAAAAATTTCAATTTTTTTTGTTGTTGGTCATGTAATGGCCAACACT
66 TTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACC
*
21659 CCCTTTTTCAGATAAAAAAATTTCAAAATTTTTTAGTGTTGGCCATGCAATGGCCGACACCCCCT
1 CCCTTTTTCAGATAAAAAAATTTCAAAATTTTTTAGTGTTGGCCATGCAATGGCCGACACCTCCT
* * * *
21724 GTTCTCAGATAAAAAAATTTTAAATTTTTTTGGTGTTGGTCATGCAATGGCCGACACC
66 TTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACC
* * * * *
21782 CCCTGTTCTCGGATAAAAAAAATTC-AAATTTTTTTGTGTAGGCCATGCAATGGCCGACACC-CC
1 CCCT-TTTTCAGATAAAAAAATTTCAAAATTTTTTAGTGTTGGCCATGCAATGGCCGACACCTCC
* * * * * * **
21845 CTTTTTCAAATAAAAAAAATTTCAAATTTTTTTAGTTTTAGCCATGTAATGGTTGACACC
65 TTTTTTCAGAT-AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACC
* * * *
21905 CCCTTTTTTAGATAAAAAATTTTCAAATTTTTTTAGTGTTGGTCATGCAATGGCCGACA--TACC
1 CCCTTTTTCAGATAAAAAAATTTCAAAATTTTTTAGTGTTGGCCATGCAATGGCCGACACCT-CC
* * *
21968 -CTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATTGCCGACACC
65 TTTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACC
* * * *
22026 CCTTTTTCTCGGATAAAAAATTTTCAAATTTTTTT
1 CCCTTTT-TCAGATAAAAAAATTTCAAAATTTTTT
22061 NNNNNNNNNN
Statistics
Matches: 340, Mismatches: 55, Indels: 14
0.83 0.13 0.03
Matches are distributed among these distances:
121 46 0.14
122 69 0.20
123 208 0.61
124 17 0.05
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (123 bp):
CCCTTTTTCAGATAAAAAAATTTCAAAATTTTTTAGTGTTGGCCATGCAATGGCCGACACCTCCT
TTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACC
Found at i:22266 original size:61 final size:59
Alignment explanation
Indices: 22171--22388 Score: 233
Period size: 61 Copynumber: 3.6 Consensus size: 59
22161 NNNNNNNNNN
* *
22171 CCATTGCATGGCCAACACAAAAAAAATTGAAATTTTTTTATCCGAAAAAAGGGTGTGTCGG
1 CCATTGCATGGCCAACAC-AAAAAATTTG-AATTTTTTTATCAGAAAAAAGGGTGTGTCGG
* * *
22232 CCATTGCATGGCCAACACAAAAAGATTTTGAATTTTTTTTATCTGAAAAAAGAGT-TGTCGA
1 CCATTGCATGGCCAACACAAAAA-A-TTTGAA-TTTTTTTATCAGAAAAAAGGGTGTGTCGG
* * * * *
22293 CCATTACATAGCCAACACCCAAAAATTTGATTTTTTTTATCAGATAAATAGGG-GTGTCGG
1 CCATTGCATGGCCAACA-CAAAAAATTTGAATTTTTTTATCAGA-AAAAAGGGTGTGTCGG
* * * *
22353 TCATTGTATGGCCAACACAAAAAAATTGTATTTTTT
1 CCATTGCATGGCCAACACAAAAAATTTGAATTTTTT
22389 ATCTGACAAA
Statistics
Matches: 131, Mismatches: 20, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
59 27 0.21
60 34 0.26
61 42 0.32
62 28 0.21
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (59 bp):
CCATTGCATGGCCAACACAAAAAATTTGAATTTTTTTATCAGAAAAAAGGGTGTGTCGG
Found at i:22367 original size:60 final size:59
Alignment explanation
Indices: 22171--22388 Score: 240
Period size: 60 Copynumber: 3.6 Consensus size: 59
22161 NNNNNNNNNN
* *
22171 CCATTGCATGGCCAACACAAAAAAAATTGAAATTTTTTTATCCGAAAAAAGGGTGTGTCGG
1 CCATTGCATGGCCAACAC-AAAAAAATTGAATTTTTTTTATCAGAAAAAAGGG-GTGTCGG
* * * * *
22232 CCATTGCATGGCCAACACAAAAAGATTTTGAATTTTTTTTATCTGAAAAAAGAGTTGTCGA
1 CCATTGCATGGCCAACACAAAAA-A-ATTGAATTTTTTTTATCAGAAAAAAGGGGTGTCGG
* * * * *
22293 CCATTACATAGCCAACACCCAAAAATTTG-ATTTTTTTTATCAGATAAATAGGGGTGTCGG
1 CCATTGCATGGCCAACA-CAAAAAAATTGAATTTTTTTTATCAGA-AAAAAGGGGTGTCGG
* * *
22353 TCATTGTATGGCCAACACAAAAAAATTGTATTTTTT
1 CCATTGCATGGCCAACACAAAAAAATTGAATTTTTT
22389 ATCTGACAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
59 23 0.17
60 40 0.30
61 40 0.30
62 29 0.22
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (59 bp):
CCATTGCATGGCCAACACAAAAAAATTGAATTTTTTTTATCAGAAAAAAGGGGTGTCGG
Found at i:27260 original size:29 final size:25
Alignment explanation
Indices: 27207--27262 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 25
27197 TCAATGATTA
*
27207 AAGTGATAAAAATGAAATTAGGACT
1 AAGTGATAAAAATAAAATTAGGACT
27232 AAGTGATAAATGAATAAATATTATGGACT
1 AAGTGATAAA--AATAAA-ATTA-GGACT
27261 AA
1 AA
27263 ATTAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 10 0.38
27 5 0.19
28 4 0.15
29 7 0.27
ACGTcount: A:0.52, C:0.04, G:0.18, T:0.27
Consensus pattern (25 bp):
AAGTGATAAAAATAAAATTAGGACT
Found at i:27590 original size:13 final size:13
Alignment explanation
Indices: 27572--27596 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27562 ATCTAAAAGA
27572 AAATAAATTAAAC
1 AAATAAATTAAAC
27585 AAATAAATTAAA
1 AAATAAATTAAA
27597 AATGATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATTAAAC
Found at i:31350 original size:2 final size:2
Alignment explanation
Indices: 31343--31376 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31333 TGTTTATACA
31343 AT AT 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 AT AT
31377 TGCAGAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33997 original size:3 final size:3
Alignment explanation
Indices: 33989--34017 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
33979 TAATCATTGT
33989 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
34018 ATCCGGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:45040 original size:24 final size:24
Alignment explanation
Indices: 45004--45054 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
44994 AAAAATAGTT
*
45004 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
45028 TTTCAATTTAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
45052 TTT
1 TTT
45055 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:46643 original size:24 final size:24
Alignment explanation
Indices: 46614--46663 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
46604 AAAAATAATC
*
46614 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTATTTAATTG
*
46638 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTAATTG
46662 TT
1 TT
46664 GACCTAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAATTG
Found at i:48234 original size:3 final size:3
Alignment explanation
Indices: 48226--48257 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
48216 TTTAAAGCAA
48226 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
48258 AGTGATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49001 original size:6 final size:6
Alignment explanation
Indices: 48992--49025 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
48982 TGCACCACCT
*
48992 CCTCTG CCTCTG CCTCTG CCTCTC CCTCT- CCTCT
1 CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CCTCT
49026 CCCTTCTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.56, G:0.09, T:0.35
Consensus pattern (6 bp):
CCTCTG
Found at i:49009 original size:12 final size:12
Alignment explanation
Indices: 48992--49029 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
48982 TGCACCACCT
*
48992 CCTCTGCCTCTG
1 CCTCTGCCTCTC
49004 CCTCTGCCTCTC
1 CCTCTGCCTCTC
49016 CCTCT-CCTCTC
1 CCTCTGCCTCTC
49027 CCT
1 CCT
49030 TCTCTCCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.00, C:0.58, G:0.08, T:0.34
Consensus pattern (12 bp):
CCTCTGCCTCTC
Found at i:53534 original size:23 final size:24
Alignment explanation
Indices: 53499--53543 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
53489 TTAAAATAAT
*
53499 ATTGAATGTTACTATGATTTTATA
1 ATTGAATGTTACTATAATTTTATA
53523 ATTGAA-GTTACTATAATTTTA
1 ATTGAATGTTACTATAATTTTA
53544 ACCGTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
ATTGAATGTTACTATAATTTTATA
Found at i:53796 original size:16 final size:15
Alignment explanation
Indices: 53769--53829 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
53759 AAACTCAAAC
53769 TTAAAACTAAAATGA
1 TTAAAACTAAAATGA
53784 TTAAAACCTAAAATGA
1 TTAAAA-CTAAAATGA
** *
53800 TTTAAATTTATAATGA
1 -TTAAAACTAAAATGA
*
53816 TTTAAACTCAAAAT
1 TTAAAACT-AAAAT
53830 TAATATGAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
15 11 0.31
16 20 0.56
17 5 0.14
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.34
Consensus pattern (15 bp):
TTAAAACTAAAATGA
Found at i:56620 original size:2 final size:2
Alignment explanation
Indices: 56613--56644 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56603 TTGATGAGGA
56613 AT 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 AT
56645 GAAATGCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56818 original size:35 final size:35
Alignment explanation
Indices: 56779--56847 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
56769 TTATTCATTA
* *
56779 ATCTACAATACATGCAATTTTATAATTAATAATAT
1 ATCTACAATACATACAATATTATAATTAATAATAT
*
56814 ATCTACAATACATACTATATTATAATTAATAATA
1 ATCTACAATACATACAATATTATAATTAATAATA
56848 ACATTGAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (35 bp):
ATCTACAATACATACAATATTATAATTAATAATAT
Found at i:67066 original size:5 final size:5
Alignment explanation
Indices: 67056--67085 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
67046 CACACAAAGA
*
67056 AAAAC AAAAC AAAAC AAAAC AAAAA AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
67086 TTCATTTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:68170 original size:122 final size:123
Alignment explanation
Indices: 67975--68196 Score: 392
Period size: 122 Copynumber: 1.8 Consensus size: 123
67965 GAAGGAAGGG
* *
67975 AGATTAATATTGTTTTTATACACAATTGTTAAGCTTTTCTTTGCCAAATAAGAAGATAAGCACAG
1 AGATTAATATTGTCTTTATACACAATTGTTAAGCCTTTCTTTGCCAAATAAGAAGATAAGCACAG
*
68040 AACTACTGAGTTGTGTG-TGGCTTAATGGTAAAGGCTAAAAGAAGGAAGGGAGATTAA
66 AACTACTGAGTTGTGTGTTGGCCTAATGGTAAAGGCTAAAAGAAGGAAGGGAGATTAA
*
68097 AGATTAATATTGTCTTTATATACAATTGTTAAGCCTTTCTTTGCCAAATAAGAAGATAAGCACAG
1 AGATTAATATTGTCTTTATACACAATTGTTAAGCCTTTCTTTGCCAAATAAGAAGATAAGCACAG
*
68162 AACTACTGAGTTGTGTGTTGGCCTGATGGTAAAGG
66 AACTACTGAGTTGTGTGTTGGCCTAATGGTAAAGG
68197 GTACTCATCG
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
122 79 0.84
123 15 0.16
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (123 bp):
AGATTAATATTGTCTTTATACACAATTGTTAAGCCTTTCTTTGCCAAATAAGAAGATAAGCACAG
AACTACTGAGTTGTGTGTTGGCCTAATGGTAAAGGCTAAAAGAAGGAAGGGAGATTAA
Found at i:69054 original size:21 final size:22
Alignment explanation
Indices: 68998--69058 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
68988 GGGGACGAAG
* *
68998 TTAAATTGTAATTTTTAAGATAA
1 TTAAATT-AAATTTTTAAGAAAA
* *
69021 TAAAAATATAATTTTTAA-AAAA
1 TTAAATTA-AATTTTTAAGAAAA
69043 TTAAATTAAATTTTTA
1 TTAAATTAAATTTTTA
69059 TATTTCAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 8 0.26
22 9 0.29
23 14 0.45
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (22 bp):
TTAAATTAAATTTTTAAGAAAA
Found at i:71150 original size:20 final size:20
Alignment explanation
Indices: 71127--71164 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
71117 CATCGAATTA
*
71127 AATATAAATTTTAAATATTT
1 AATATAAATTGTAAATATTT
*
71147 AATATTAATTGTAAATAT
1 AATATAAATTGTAAATAT
71165 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AATATAAATTGTAAATATTT
Found at i:78124 original size:86 final size:86
Alignment explanation
Indices: 77979--78152 Score: 339
Period size: 86 Copynumber: 2.0 Consensus size: 86
77969 ATGAAGGTGG
77979 TTACCTGGTATTCGTTTTCACGCTCTTTCAAACTCTTAGAAAGGTCCTCAACTCTCTTTTTCAGA
1 TTACCTGGTATTCGTTTTCACGCTCTTTCAAACTCTTAGAAAGGTCCTCAACTCTCTTTTTCAGA
78044 TCAGCTGCTCCTTCTTTAGAC
66 TCAGCTGCTCCTTCTTTAGAC
*
78065 TTACCTGGTATTCGTTTTCACGCTCTTTCAAACTCTTAGAAAGGTCCTCCACTCTCTTTTTCAGA
1 TTACCTGGTATTCGTTTTCACGCTCTTTCAAACTCTTAGAAAGGTCCTCAACTCTCTTTTTCAGA
78130 TCAGCTGCTCCTTCTTTAGAC
66 TCAGCTGCTCCTTCTTTAGAC
78151 TT
1 TT
78153 TTGCACAGCA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.19, C:0.28, G:0.13, T:0.40
Consensus pattern (86 bp):
TTACCTGGTATTCGTTTTCACGCTCTTTCAAACTCTTAGAAAGGTCCTCAACTCTCTTTTTCAGA
TCAGCTGCTCCTTCTTTAGAC
Found at i:80251 original size:20 final size:21
Alignment explanation
Indices: 80218--80257 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
80208 TTCGGACACA
*
80218 TTCATCTTCACTTCATTTTAT
1 TTCATCTTCACTTCAATTTAT
*
80239 TTCA-CTTCGCTTCAATTTA
1 TTCATCTTCACTTCAATTTA
80258 ATTTTAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.20, C:0.25, G:0.03, T:0.53
Consensus pattern (21 bp):
TTCATCTTCACTTCAATTTAT
Found at i:82058 original size:14 final size:14
Alignment explanation
Indices: 82035--82073 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
82025 ATACTCAAAC
82035 TTAT-TTAATTTGT
1 TTATATTAATTTGT
*
82048 TTATATTAATTTAT
1 TTATATTAATTTGT
82062 TTATATT-ATTTG
1 TTATATTAATTTG
82074 ATATCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
TTATATTAATTTGT
Found at i:83398 original size:22 final size:22
Alignment explanation
Indices: 83366--83407 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
83356 TATTTTTAAG
83366 AAACACATTTGAAATAAAAAAA
1 AAACACATTTGAAATAAAAAAA
* *
83388 AAACACTTTTGAGATAAAAA
1 AAACACATTTGAAATAAAAA
83408 CAATACTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (22 bp):
AAACACATTTGAAATAAAAAAA
Found at i:85989 original size:13 final size:13
Alignment explanation
Indices: 85971--86000 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
85961 TTAAAATTTG
85971 AATTCGAATTTAA
1 AATTCGAATTTAA
*
85984 AATTCGAGTTTAA
1 AATTCGAATTTAA
85997 AATT
1 AATT
86001 AAAAAATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (13 bp):
AATTCGAATTTAA
Found at i:94126 original size:19 final size:20
Alignment explanation
Indices: 94102--94139 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
94092 TAATTTTTTA
*
94102 ATTTAATTTGAAT-AAATTT
1 ATTTAATTTAAATCAAATTT
94121 ATTTAATTTAAATCAAATT
1 ATTTAATTTAAATCAAATT
94140 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTTAATTTAAATCAAATTT
Found at i:94580 original size:54 final size:55
Alignment explanation
Indices: 94478--94594 Score: 148
Period size: 55 Copynumber: 2.2 Consensus size: 55
94468 CAAAAATTTG
*
94478 AAAAAAAA-TTTGGTGTTAGTCATTGCATGACCGACACCCCCTTTTTTATCTGAC
1 AAAAAAAATTTTGGTGTTAGCCATTGCATGACCGACACCCCCTTTTTTATCTGAC
* * * * * * *
94532 AGAAAAAATTTTGGTGTTGGCCATTGCATGGCTGACACTCCC-TTTTTATTTGAT
1 AAAAAAAATTTTGGTGTTAGCCATTGCATGACCGACACCCCCTTTTTTATCTGAC
94586 AAAAAAAAT
1 AAAAAAAAT
94595 CAAATTTTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 25 0.47
55 28 0.53
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (55 bp):
AAAAAAAATTTTGGTGTTAGCCATTGCATGACCGACACCCCCTTTTTTATCTGAC
Found at i:94660 original size:59 final size:59
Alignment explanation
Indices: 94540--94795 Score: 232
Period size: 59 Copynumber: 4.3 Consensus size: 59
94530 ACAGAAAAAA
* * **
94540 TTTTGGTGTTGGCCATTGC-ATGGCTGACACTCC-CTTTTTATTTGATAAAAAAAATCAAATT
1 TTTTAGTGTTGGCCA-TGCAATGGCCGACAC-CCTCTTTTT-TCAGAT-AAAAAAATCAAATT
* * * * *
94601 TTTGAGTATTGCCCATGCAATGGTCGACACCCTCTTTTTGTCAGATAAAAAATTC-AATT
1 TTTTAGTGTTGGCCATGCAATGGCCGACACCCTCTTTTT-TCAGATAAAAAAATCAAATT
* * * * * *
94660 TTTTAGTGTTGGTCATGCCATGACCGACACCCT-TATTTACTGATAAAAAAATCAAATT
1 TTTTAGTGTTGGCCATGCAATGGCCGACACCCTCTTTTTTCAGATAAAAAAATCAAATT
* * *
94718 TTTTTGTGTCGGCCATGCAATGGCCGACACTCTCTTTTTTCAGATAAAAAAATTTCAAAATT
1 TTTTAGTGTTGGCCATGCAATGGCCGACACCCTCTTTTTTCAGATAAAAAAA--TC-AAATT
* *
94780 TTTTGGTATTGGCCAT
1 TTTTAGTGTTGGCCAT
94796 ACCCTTTTTA
Statistics
Matches: 155, Mismatches: 33, Indels: 13
0.77 0.16 0.06
Matches are distributed among these distances:
57 12 0.08
58 35 0.23
59 45 0.29
60 13 0.08
61 32 0.21
62 18 0.12
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (59 bp):
TTTTAGTGTTGGCCATGCAATGGCCGACACCCTCTTTTTTCAGATAAAAAAATCAAATT
Found at i:94913 original size:55 final size:58
Alignment explanation
Indices: 94826--94976 Score: 159
Period size: 59 Copynumber: 2.6 Consensus size: 58
94816 AATTCAAATG
* * * **
94826 GCATGGTCGACACCACCTTTTTTTCTAGT-AAAAA-TT-ATTTTTTTTGTTAGCCA-T
1 GCATGGCCGACACCTCCTTTTTGTCTAGTAAAAAATTTAATTTTTGATGTTAGCCATT
94880 GCAATGGCCGACACCTCCTTTTTGTC-AGATAAAAAATTTGAATTTTTGATGTTAGCCATT
1 GC-ATGGCCGACACCTCCTTTTTGTCTAG-TAAAAAATTT-AATTTTTGATGTTAGCCATT
* * *
94940 GCATGGCCGATACCTCCTTTTTAATCTGGTAAAAAAT
1 GCATGGCCGACACCTCCTTTTT-GTCTAGTAAAAAAT
94977 CAACTTTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
54 4 0.05
55 21 0.26
56 5 0.06
57 2 0.03
59 34 0.43
60 13 0.16
61 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (58 bp):
GCATGGCCGACACCTCCTTTTTGTCTAGTAAAAAATTTAATTTTTGATGTTAGCCATT
Found at i:94985 original size:59 final size:58
Alignment explanation
Indices: 94828--95052 Score: 150
Period size: 59 Copynumber: 3.9 Consensus size: 58
94818 TTCAAATGGC
* * * **
94828 ATGGTCGACACCACCTTTTTTTCTAG-T-AAAAATT--ATTTTTTTTGTTAGCCATGCA
1 ATGGCCGACACCTCCTTTTTATC-AGATAAAAAATTCAATTTTTGATGTTAGCCATGCA
* *
94883 ATGGCCGACACCTCCTTTTTGTCAGATAAAAAATTTGAATTTTTGATGTTAGCCATTGC-
1 ATGGCCGACACCTCCTTTTTATCAGATAAAAAA-TTCAATTTTTGATGTTAGCCA-TGCA
* * * *
94942 ATGGCCGATACCTCCTTTTTAATCTGGTAAAAAA-TCAACTTTTTTTG-TGTT-GACTATGCA
1 ATGGCCGACACCTCCTTTTT-ATCAGATAAAAAATTCAA---TTTTTGATGTTAG-CCATGCA
** * *
95002 ATGATCGACACC-CCTTTTTATCTGAATAAAAAA-TAAATTTTTG-TG-TAGCCA
1 ATGGCCGACACCTCCTTTTTATCAG-ATAAAAAATTCAATTTTTGATGTTAGCCA
95053 ATTTTTGTCA
Statistics
Matches: 139, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
54 2 0.01
55 24 0.17
56 14 0.10
57 2 0.01
58 8 0.06
59 55 0.40
60 28 0.20
61 6 0.04
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (58 bp):
ATGGCCGACACCTCCTTTTTATCAGATAAAAAATTCAATTTTTGATGTTAGCCATGCA
Found at i:96009 original size:30 final size:30
Alignment explanation
Indices: 95969--96090 Score: 135
Period size: 30 Copynumber: 4.1 Consensus size: 30
95959 AAAAAATAAT
* *
95969 AATTAGAATATAAAGGAAATTAGAAATTAA
1 AATTAAAATATAAACGAAATTAGAAATTAA
95999 AATTAAAATATACAA-GAAATTAGAAATTAA
1 AATTAAAATATA-AACGAAATTAGAAATTAA
* * *
96029 ATTTAAAATAAAAACGAAATTACAAATTAA
1 AATTAAAATATAAACGAAATTAGAAATTAA
* *
96059 ATTTAAAA-AGTAAACGAAA--AAAAATTAA
1 AATTAAAATA-TAAACGAAATTAGAAATTAA
96087 AATT
1 AATT
96091 GAGTAGATCC
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
28 11 0.13
29 3 0.04
30 66 0.80
31 2 0.02
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.26
Consensus pattern (30 bp):
AATTAAAATATAAACGAAATTAGAAATTAA
Found at i:97299 original size:20 final size:20
Alignment explanation
Indices: 97256--97299 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
97246 TTTTAAATCG
* * * *
97256 AAAATATAAAAAACATTTTG
1 AAAATAGAAAAAAAATTGTA
97276 AAAATAGAAAAAAAATTGTA
1 AAAATAGAAAAAAAATTGTA
97296 AAAA
1 AAAA
97300 ATTCAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAATAGAAAAAAAATTGTA
Found at i:119384 original size:24 final size:24
Alignment explanation
Indices: 119352--119400 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
119342 ATGATTAAGA
119352 GAAGGGTGTGGCTTAATGGCATGT
1 GAAGGGTGTGGCTTAATGGCATGT
119376 GAAGGGTGTGGCTTAATGGCATGT
1 GAAGGGTGTGGCTTAATGGCATGT
119400 G
1 G
119401 GCCGCTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.43, T:0.29
Consensus pattern (24 bp):
GAAGGGTGTGGCTTAATGGCATGT
Found at i:133376 original size:20 final size:20
Alignment explanation
Indices: 133351--133388 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
133341 TCATATCAGT
* *
133351 AATTTTATTTTGAATTTTAA
1 AATTTTAATTTAAATTTTAA
133371 AATTTTAATTTAAATTTT
1 AATTTTAATTTAAATTTT
133389 TAATATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTTAATTTAAATTTTAA
Found at i:136989 original size:29 final size:29
Alignment explanation
Indices: 136928--137006 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
136918 AAATTTTAAA
* *
136928 TTAATAATAATAAAATTATACTTTAATCC
1 TTAAAAATAATAAAATTATACATTAATCC
136957 -TAAAAATAATATAAATT-TA-ATTAATCC
1 TTAAAAATAATA-AAATTATACATTAATCC
* *
136984 TTTAAAAATTATAAAAATATACA
1 -TTAAAAATAATAAAATTATACA
137007 CGTTACTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
27 7 0.17
28 16 0.39
29 17 0.41
30 1 0.02
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAAAATAATAAAATTATACATTAATCC
Found at i:141326 original size:2 final size:2
Alignment explanation
Indices: 141319--141350 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
141309 TCTTTTAATA
141319 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
141351 GTATGCAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:149623 original size:24 final size:24
Alignment explanation
Indices: 149596--149651 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
149586 ATTTAAGACG
149596 AGATTTGGGGTTGTTTTT-ATTTAA
1 AGATTTGGGGTTGTTTTTAATTT-A
* * *
149620 AGA-TTGGGTTTTTTTTTAATTTG
1 AGATTTGGGGTTGTTTTTAATTTA
149643 AGATTTGGG
1 AGATTTGGG
149652 AATGTGAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.54
Consensus pattern (24 bp):
AGATTTGGGGTTGTTTTTAATTTA
Done.