Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013493.1 Kokia drynarioides strain JFW-HI SEQ_128519, 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: 101423
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:1183 original size:7 final size:6
Alignment explanation
Indices: 1167--1208 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
1157 TAATATTCAA
*
1167 TTTTTC TTTTTC TTTTT- TTATTAC TTTCTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTT-TTC TTTTTC TTTTT
1209 ACGAATGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 2 0.06
6 22 0.71
7 7 0.23
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:1188 original size:25 final size:25
Alignment explanation
Indices: 1160--1208 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1150 TTTAAACTAA
1160 TATTCAATTT-TTCTTTTTCTTTTTT
1 TATT-AATTTCTTCTTTTTCTTTTTT
*
1185 TATTACTTTCTTCTTTTTCTTTTT
1 TATTAATTTCTTCTTTTTCTTTTT
1209 ACGAATGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (25 bp):
TATTAATTTCTTCTTTTTCTTTTTT
Found at i:5581 original size:19 final size:19
Alignment explanation
Indices: 5546--5596 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
5536 AATATGCATT
*
5546 TAAATAATAAAATTTAA-AA
1 TAAAT-ATAAAACTTAAGAA
5565 TAAATATAAAACCTTAAGAA
1 TAAATATAAAA-CTTAAGAA
*
5585 AATAATATAAAA
1 TA-AATATAAAA
5597 TTTTGCACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.22
19 9 0.33
20 3 0.11
21 9 0.33
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAATATAAAACTTAAGAA
Found at i:5953 original size:30 final size:30
Alignment explanation
Indices: 5834--6007 Score: 99
Period size: 28 Copynumber: 5.7 Consensus size: 30
5824 GGGTTTAAAT
*
5834 TTTTATTTTTTTTAATTTTTAAGGGTCTCAAA
1 TTTT-TTTTTTTTAATTTTTAAGGAT-TCAAA
*
5866 ---ATTTTTTTTAATTTTTATAGG-TT-AAA
1 TTTTTTTTTTTTAATTTTTA-AGGATTCAAA
** * *** *
5892 -TTTTTTTTACTAACTTTTAAGGGGCCTAA
1 TTTTTTTTTTTTAATTTTTAAGGATTCAAA
5921 TTTTTTTTTTTTAATTTTTAAGGATTCAAA
1 TTTTTTTTTTTTAATTTTTAAGGATTCAAA
*
5951 TTTAATTTTTTTTTACCAATTTTTAAGAGATTTAAAA
1 TTT--TTTTTTTTT---AATTTTTAAG-GA-TTCAAA
* * *
5988 ATTTTTTTCTCTAATTTTTA
1 TTTTTTTTTTTTAATTTTTA
6008 TTATTTTAAT
Statistics
Matches: 110, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
26 3 0.03
27 4 0.04
28 30 0.27
29 5 0.05
30 25 0.23
32 17 0.15
35 17 0.15
36 2 0.02
37 7 0.06
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (30 bp):
TTTTTTTTTTTTAATTTTTAAGGATTCAAA
Found at i:5960 original size:32 final size:30
Alignment explanation
Indices: 5924--6007 Score: 80
Period size: 32 Copynumber: 2.6 Consensus size: 30
5914 GGCCTAATTT
5924 TTTTTTTTTAATTTTTAAG-GATTCAAATTTAA
1 TTTTTTTTTAATTTTTAAGAGATTCAAA---AA
*
5956 TTTTTTTTTACCAATTTTTAAGAGATTTAAAAA
1 TTTTTTTTT---AATTTTTAAGAGATTCAAAAA
5989 TTTTTTTCTCTAATTTTTA
1 TTTTTTT-T-TAATTTTTA
6008 TTATTTTAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
32 17 0.38
33 9 0.20
34 1 0.02
35 11 0.24
36 7 0.16
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTTTTTTTAATTTTTAAGAGATTCAAAAA
Found at i:5995 original size:35 final size:31
Alignment explanation
Indices: 5919--5995 Score: 73
Period size: 35 Copynumber: 2.3 Consensus size: 31
5909 TAAGGGGCCT
*
5919 AATTTTTTTTTTTTAATTTTTAAGGATTCAAA
1 AATTTTTTTTTTTCAATTTTTAAGGATT-AAA
**
5951 TTTAATTTTTTTTTACCAATTTTTAAGAGATTTAAA
1 ---AATTTTTTTTTTTCAATTTTTAAG-GA-TTAAA
5987 AATTTTTTT
1 AATTTTTTT
5996 CTCTAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 9 0.24
35 21 0.57
36 5 0.14
37 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (31 bp):
AATTTTTTTTTTTCAATTTTTAAGGATTAAA
Found at i:6734 original size:153 final size:150
Alignment explanation
Indices: 6450--6836 Score: 550
Period size: 153 Copynumber: 2.5 Consensus size: 150
6440 CTTCTTCTTT
* *
6450 TTTTTTTTTTTGTAATTTGATGTTTTAGGACCTTATTTGCATTTTAAATTTAATTTTGAAGATCT
1 TTTTTTTTTTT-TAATTTGATGTTTTAGGATCTTATTTGCATTTTTAATTTAATTTTGAAGATCT
*
6515 ATATGATGCTTATTATTTGAATTATGATTTAATTCATTTGTTTGTGTTTCCTGAATTTTGAATCT
65 ATATGAT--AT-TTATTT---TTATGATTTAATTCATTTGTTTGTGTTTCCTGAATTTTGAATCT
6580 TTCGTTTTGTTCGTTATTACTGTTTCC
124 TTCGTTTTGTTCGTTATTACTGTTTCC
* * *
6607 TTTTTTTTTTTATAATTTGATGTTTTAGGATTTTATTTGCATTTTTTATTTTAATTTCGAAGATC
1 TTTTTTTTTTT-TAATTTGATGTTTTAGGATCTTATTTGCA-TTTTTAATTTAATTTTGAAGATC
* *
6672 TATATGATATTTATTTTTCATGATTTAATTCATTTGTTTGTGTTTCCTGGATTTTGATTCTTTCG
64 TATATGATATTTATTTTT-ATGATTTAATTCATTTGTTTGTGTTTCCTGAATTTTGAATCTTTCG
*
6737 TTTTGTTCGTTGTTACTGTTTCC
128 TTTTGTTCGTTATTACTGTTTCC
6760 ----TTTTTTTTAATTTGATGTTTT-GGAATCTTATTTGCATTTTTAATTTAATTTTGAAGATCT
1 TTTTTTTTTTTTAATTTGATGTTTTAGG-ATCTTATTTGCATTTTTAATTTAATTTTGAAGATCT
*
6820 ATATGATGTTTATTTTT
65 ATATGATATTTATTTTT
6837 TGAATTATGA
Statistics
Matches: 213, Mismatches: 14, Indels: 16
0.88 0.06 0.07
Matches are distributed among these distances:
147 40 0.19
148 25 0.12
149 7 0.03
152 2 0.01
153 66 0.31
155 6 0.03
156 1 0.00
157 38 0.18
158 28 0.13
ACGTcount: A:0.20, C:0.08, G:0.13, T:0.59
Consensus pattern (150 bp):
TTTTTTTTTTTTAATTTGATGTTTTAGGATCTTATTTGCATTTTTAATTTAATTTTGAAGATCTA
TATGATATTTATTTTTATGATTTAATTCATTTGTTTGTGTTTCCTGAATTTTGAATCTTTCGTTT
TGTTCGTTATTACTGTTTCC
Found at i:7016 original size:15 final size:16
Alignment explanation
Indices: 6993--7022 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6983 TATTGACTTT
6993 TTTTGTTTTATATGAG
1 TTTTGTTTTATATGAG
7009 TTTT-TTTTATATGA
1 TTTTGTTTTATATGA
7023 ATATTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (16 bp):
TTTTGTTTTATATGAG
Found at i:15972 original size:107 final size:106
Alignment explanation
Indices: 15839--16071 Score: 281
Period size: 106 Copynumber: 2.2 Consensus size: 106
15829 ACGACAAATG
**
15839 CATTATATTTCTTCATGTTATTGCTTACTCATGCATCACCTAGCAAGGGGTACATCA-AGGTTTG
1 CATTATATTTCTTCATGTTACCGCTTACTCATGCATCACCTAGCAAGGGGTACATCACA--TTTG
* * * *
15903 CATGCTCATTATTGCTTACTCAATG-TAGACAGCATGACCGAGA
64 CATACTCATTACTGCTTACTCAATGCT-GACAACATGACCAAGA
* * * * * *
15946 CATTATATTTCTTCATGTTACCGCTTACTCTTGGATCGCCTAGGAAGGGTTACATTACATTTGCA
1 CATTATATTTCTTCATGTTACCGCTTACTCATGCATCACCTAGCAAGGGGTACATCACATTTGCA
* ** *
16011 TACTCATTGCTGCTTACTTGATGCTGACAACATGACCAAGG
66 TACTCATTACTGCTTACTCAATGCTGACAACATGACCAAGA
16052 CATTATATTTCTTCATGTTA
1 CATTATATTTCTTCATGTTA
16072 TTGCTCAAGA
Statistics
Matches: 108, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
106 57 0.53
107 50 0.46
108 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (106 bp):
CATTATATTTCTTCATGTTACCGCTTACTCATGCATCACCTAGCAAGGGGTACATCACATTTGCA
TACTCATTACTGCTTACTCAATGCTGACAACATGACCAAGA
Found at i:16066 original size:106 final size:107
Alignment explanation
Indices: 15663--16076 Score: 413
Period size: 107 Copynumber: 3.9 Consensus size: 107
15653 TGTTCCTGTT
* * * * *
15663 CATCGCCTAGGAAGGGGTACATCA-GGTTCGCATACCCATTATTGCCTACTTGATGTGGACAACA
1 CATCGCCTAGGAAGGGGTACATCACAGTTTGCATACTCATTATTGCTTACTTGATGTAGACAACA
* * *
15727 TGACCAATGCATTATATTTCTTTATGTCATTTGCTTACT-TGTG
66 TGACCAAGGCATTATATTTCTTCATGTTA-TTGCTTACTCT-TG
* * *
15770 CATCGCATAGGAAGGGGTTCAT--CAGTTTCGTATACTCATTAGTT-CTTACTTG-TCGTA-AC-
1 CATCGCCTAGGAAGGGGTACATCACAGTTT-GCATACTCATTA-TTGCTTACTTGAT-GTAGACA
* * *
15829 AC--GACAAATGCATTATATTTCTTCATGTTATTGCTTACTCATG
63 ACATGACCAAGGCATTATATTTCTTCATGTTATTGCTTACTCTTG
* * * ** *
15872 CATCACCTAGCAAGGGGTACATCA-AGGTTTGCATGCTCATTATTGCTTACTCAATGTAGACAGC
1 CATCGCCTAGGAAGGGGTACATCACA-GTTTGCATACTCATTATTGCTTACTTGATGTAGACAAC
* * **
15936 ATGACCGAGACATTATATTTCTTCATGTTACCGCTTACTCTTG
65 ATGACCAAGGCATTATATTTCTTCATGTTATTGCTTACTCTTG
* * * **
15979 GATCGCCTAGGAAGGGTTACATTACA-TTTGCATACTCATTGCTGCTTACTTGATGCT-GACAAC
1 CATCGCCTAGGAAGGGGTACATCACAGTTTGCATACTCATTATTGCTTACTTGATG-TAGACAAC
16042 ATGACCAAGGCATTATATTTCTTCATGTTATTGCT
65 ATGACCAAGGCATTATATTTCTTCATGTTATTGCT
16077 CAAGAGTAAG
Statistics
Matches: 248, Mismatches: 43, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
102 31 0.12
103 45 0.18
104 7 0.03
105 3 0.01
106 66 0.27
107 93 0.38
108 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (107 bp):
CATCGCCTAGGAAGGGGTACATCACAGTTTGCATACTCATTATTGCTTACTTGATGTAGACAACA
TGACCAAGGCATTATATTTCTTCATGTTATTGCTTACTCTTG
Found at i:19706 original size:6 final size:6
Alignment explanation
Indices: 19695--19726 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
19685 CATGAGGACC
19695 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT
19727 TTAACATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:28341 original size:13 final size:13
Alignment explanation
Indices: 28310--28353 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
28300 ACTTGAACCC
*
28310 TGAACCTTAAACT
1 TGAACCTCAAACT
** *
28323 CAAACCTCGAACT
1 TGAACCTCAAACT
28336 TGAACCTCAAACT
1 TGAACCTCAAACT
28349 TGAAC
1 TGAAC
28354 TTAGAACCCT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.39, C:0.30, G:0.09, T:0.23
Consensus pattern (13 bp):
TGAACCTCAAACT
Found at i:28360 original size:20 final size:20
Alignment explanation
Indices: 28321--28361 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
28311 GAACCTTAAA
28321 CTCAAACCTCGAACTTGAAC
1 CTCAAACCTCGAACTTGAAC
*
28341 CTCAAA-CTTGAACTTAGAAC
1 CTCAAACCTCGAACTT-GAAC
28361 C
1 C
28362 CTGAACTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (20 bp):
CTCAAACCTCGAACTTGAAC
Found at i:32710 original size:17 final size:19
Alignment explanation
Indices: 32688--32726 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
32678 CAATTTAACT
32688 TGTTTTC-T-TTCAAATTA
1 TGTTTTCATATTCAAATTA
*
32705 TGTTTTCATATTGAAATTA
1 TGTTTTCATATTCAAATTA
32724 TGT
1 TGT
32727 AATTATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (19 bp):
TGTTTTCATATTCAAATTA
Found at i:38626 original size:13 final size:14
Alignment explanation
Indices: 38601--38641 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
38591 AGATCTCGAA
38601 CTCGAACTCTAAATC
1 CTCGAA-TCTAAATC
38616 CT-GAATCTAAAT-
1 CTCGAATCTAAATC
*
38628 CTCGAATTTAAATC
1 CTCGAATCTAAATC
38642 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 2 0.09
13 16 0.70
14 3 0.13
15 2 0.09
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (14 bp):
CTCGAATCTAAATC
Found at i:38631 original size:27 final size:27
Alignment explanation
Indices: 38601--38663 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
38591 AGATCTCGAA
* *
38601 CTCGAACTCTAAATCCTGAA-TCTAAAT
1 CTCGAA-TCTAAATCATAAATTCTAAAT
* *
38628 CTCGAATTTAAATCATAAATTTTAAAT
1 CTCGAATCTAAATCATAAATTCTAAAT
38655 CTCGAATCT
1 CTCGAATCT
38664 CAACCCTAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (27 bp):
CTCGAATCTAAATCATAAATTCTAAAT
Found at i:40911 original size:31 final size:32
Alignment explanation
Indices: 40858--40926 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
40848 ATGGTTATTT
*
40858 AACTA-TCGAAAGTTTTTCATTTAAGTCATTA
1 AACTATTCGAAAATTTTTCATTTAAGTCATTA
40889 AACTATTCGAAAATTTTT-ATTTAAGTCATTA
1 AACTATTCGAAAATTTTTCATTTAAGTCATTA
*
40920 GACTATT
1 AACTATT
40927 AGATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (32 bp):
AACTATTCGAAAATTTTTCATTTAAGTCATTA
Found at i:46702 original size:24 final size:24
Alignment explanation
Indices: 46660--46715 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
46650 AAAATACATA
*
46660 AATATTTTAAAAATATATAATAAT
1 AATATTTAAAAAATATATAATAAT
46684 AA-ATTTAAAAAATATTATAATAAT
1 AATATTTAAAAAATA-TATAATAAT
46708 AATATTTA
1 AATATTTA
46716 GAATGTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 11 0.38
24 13 0.45
25 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AATATTTAAAAAATATATAATAAT
Found at i:49482 original size:15 final size:15
Alignment explanation
Indices: 49462--49515 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
49452 ATACTACAAA
49462 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
49477 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
49494 AAATATTTACTATTAAT
1 --ATATTTATTATTAAT
49511 ATATT
1 ATATT
49516 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 8 0.25
18 1 0.03
19 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:52247 original size:20 final size:20
Alignment explanation
Indices: 52213--52273 Score: 76
Period size: 18 Copynumber: 3.2 Consensus size: 20
52203 TGAACTGATT
52213 TATTTAAAATAATGAAAATA
1 TATTTAAAATAATGAAAATA
52233 TATTATAAAAT-ATG--AATA
1 TATT-TAAAATAATGAAAATA
*
52251 TATTTAAAATAATTAAAA-A
1 TATTTAAAATAATGAAAATA
52270 TATT
1 TATT
52274 AAATTGATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 6 0.17
18 10 0.28
19 5 0.14
20 9 0.25
21 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
TATTTAAAATAATGAAAATA
Found at i:53276 original size:2 final size:2
Alignment explanation
Indices: 53263--53292 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53253 ATATAGTAAA
*
53263 AT AT AT AA 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
53293 TAAAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:59422 original size:5 final size:5
Alignment explanation
Indices: 59412--59437 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
59402 TCTAGGTAAT
59412 AAAAC AAAAC AAAAC AAAAC AAAAC A
1 AAAAC AAAAC AAAAC AAAAC AAAAC A
59438 TGCATTTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:60645 original size:40 final size:38
Alignment explanation
Indices: 60600--60687 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 38
60590 TAATATTTTT
*
60600 TATTTTTAATAAAATCATATC-TAAAATAATTTTTAATATA
1 TATTTTTAATAAAATCAT-TCATAAAATAA-TTATAAT-TA
* *
60640 TATTTTTAATTAATATTATTCATAAAATAATTATAATTA
1 TATTTTTAA-TAAAATCATTCATAAAATAATTATAATTA
60679 -ATTTTTAAT
1 TATTTTTAAT
60688 TATATATTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 1 0.02
38 8 0.19
39 2 0.05
40 17 0.40
41 15 0.35
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.51
Consensus pattern (38 bp):
TATTTTTAATAAAATCATTCATAAAATAATTATAATTA
Found at i:68947 original size:19 final size:20
Alignment explanation
Indices: 68920--68957 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
68910 AATTTCATGA
68920 ATTACTTAT-TTATTTTATC
1 ATTACTTATATTATTTTATC
*
68939 ATTATTTATATTATTTTAT
1 ATTACTTATATTATTTTAT
68958 TGAGTTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTACTTATATTATTTTATC
Found at i:72315 original size:15 final size:16
Alignment explanation
Indices: 72279--72318 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
72269 ATAGTAAAAA
72279 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
72296 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
72311 TATAATTT
1 TATAATTT
72319 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:72688 original size:15 final size:16
Alignment explanation
Indices: 72668--72698 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
72658 AAAATAAGTT
72668 TTTTATTT-ATTTAAG
1 TTTTATTTAATTTAAG
72683 TTTTATTTAATTTAAG
1 TTTTATTTAATTTAAG
72699 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTATTTAATTTAAG
Found at i:74329 original size:9 final size:9
Alignment explanation
Indices: 74301--74404 Score: 51
Period size: 9 Copynumber: 11.3 Consensus size: 9
74291 ATAATTAATT
*
74301 AAATTTTAA
1 AAATATTAA
74310 TAAATTATTAA
1 -AAA-TATTAA
74321 AAATATTAA
1 AAATATTAA
74330 TTATAA-ATTATA
1 --A-AATATTA-A
74342 AAA-ATTAA
1 AAATATTAA
74350 AAATTATT-A
1 AAA-TATTAA
74359 AAAT-TTATA
1 AAATATTA-A
*
74368 ACA-A-TAA
1 AAATATTAA
*
74375 AAATAGTAA
1 AAATATTAA
74384 AAATATTAA
1 AAATATTAA
74393 AAA-ATTAGA
1 AAATATTA-A
74402 AAA
1 AAA
74405 AAATACAAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 27
0.71 0.04 0.25
Matches are distributed among these distances:
7 5 0.06
8 12 0.16
9 37 0.48
10 10 0.13
11 10 0.13
12 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (9 bp):
AAATATTAA
Found at i:74347 original size:16 final size:17
Alignment explanation
Indices: 74328--74368 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
74318 TAAAAATATT
74328 AATTATAAATTA-TAAA
1 AATTATAAATTATTAAA
*
74344 AATTAAAAATTATTAAA
1 AATTATAAATTATTAAA
*
74361 ATTTATAA
1 AATTATAA
74369 CAATAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTATAAATTATTAAA
Found at i:74366 original size:26 final size:27
Alignment explanation
Indices: 74287--74404 Score: 84
Period size: 25 Copynumber: 4.3 Consensus size: 27
74277 TATATGTTAT
* * *
74287 ATTAATAATTAATTAAATTTTAATAAATT
1 ATTAAAAATTAATTAAAATTT-ATAAA-A
74316 ATTAAAAATATTAATTATAAA-TTATAAAA
1 ATT-AAAA-ATTAATTA-AAATTTATAAAA
*
74345 ATTAAAAATT-ATTAAAATTTATAACA
1 ATTAAAAATTAATTAAAATTTATAAAA
* *
74371 A-TAAAAA-TAGTAAAAATATTA-AAAA
1 ATTAAAAATTAATTAAAAT-TTATAAAA
74396 ATTAGAAAA
1 ATTA-AAAA
74405 AAATACAAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
24 1 0.01
25 19 0.26
26 17 0.23
27 7 0.09
28 4 0.05
29 6 0.08
30 8 0.11
31 10 0.14
32 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (27 bp):
ATTAAAAATTAATTAAAATTTATAAAA
Found at i:79848 original size:20 final size:20
Alignment explanation
Indices: 79823--79860 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
79813 GATTTCTCGA
79823 AAAAAGTCAAT-GGTCAACCC
1 AAAAAGTC-ATCGGTCAACCC
79843 AAAAAGTCATCGGTCAAC
1 AAAAAGTCATCGGTCAAC
79861 AGTCAATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAAAGTCATCGGTCAACCC
Found at i:89459 original size:21 final size:21
Alignment explanation
Indices: 89417--89460 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
89407 ATTTCTTTTT
*
89417 AAATAAAACACCAAAAATATA
1 AAATAAAACACCAAAAAAATA
*
89438 AAATAAAACA-GAAAATAAATA
1 AAATAAAACACCAAAA-AAATA
89459 AA
1 AA
89461 TATATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.14
Consensus pattern (21 bp):
AAATAAAACACCAAAAAAATA
Found at i:89614 original size:18 final size:18
Alignment explanation
Indices: 89575--89613 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
89565 AATGTTTTTT
89575 AAAAGTATTTTTGACATA
1 AAAAGTATTTTTGACATA
89593 AAAAGTATTTTTGA-ATA
1 AAAAGTATTTTTGACATA
89610 AAAA
1 AAAA
89614 ACAATGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (18 bp):
AAAAGTATTTTTGACATA
Found at i:90913 original size:29 final size:28
Alignment explanation
Indices: 90847--90915 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
90837 TTTAATATAC
*
90847 TATATTTTTATAATTTTTAAGGATTAAG
1 TATAATTTTATAATTTTTAAGGATTAAG
*
90875 T-TAAATTTT-TATATTTTTAGGGGATTAAAG
1 TAT-AATTTTATA-ATTTTTA-AGGATT-AAG
90905 TATAATTTTAT
1 TATAATTTTAT
90916 CTTTATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
27 3 0.09
28 13 0.39
29 5 0.15
30 10 0.30
31 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (28 bp):
TATAATTTTATAATTTTTAAGGATTAAG
Found at i:97434 original size:24 final size:25
Alignment explanation
Indices: 97392--97439 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
97382 AGGTGCTTTT
*
97392 TCAGCAACTACAGTCACAT-TTTAA
1 TCAGCAACAACAGTCACATGTTTAA
97416 TCAGCAACAACAG-CTACATGTTTA
1 TCAGCAACAACAGTC-ACATGTTTA
97440 CACATTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 16 0.76
25 4 0.19
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (25 bp):
TCAGCAACAACAGTCACATGTTTAA
Found at i:101082 original size:6 final size:6
Alignment explanation
Indices: 101071--101104 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
101061 AGTCGAGCTG
101071 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGG
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGG
101105 GGGAGACCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
GAGGAA
Done.