Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009610.1 Kokia drynarioides strain JFW-HI SEQ_124326, 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: 86403
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:368 original size:16 final size:16
Alignment explanation
Indices: 323--372 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
313 TAAACCTAGC
*
323 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
339 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
353 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
369 TAAT
1 TAAT
373 ATCCTCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:1704 original size:43 final size:42
Alignment explanation
Indices: 1650--1743 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
1640 ATTAACATGT
* *
1650 TAAACTATATTACTTGACTCGTGTTAATATGATTG-CATGTTA
1 TAAATTATATTACTTGACTCGTATTAATAT-ATTGACATGTTA
* * *
1692 CTAAATTATATTACTTTACTCTTATTAATATTTTGACATGTTA
1 -TAAATTATATTACTTGACTCGTATTAATATATTGACATGTTA
*
1735 TTAATTATA
1 TAAATTATA
1744 CAGTTCATCT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 11 0.25
43 33 0.75
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.48
Consensus pattern (42 bp):
TAAATTATATTACTTGACTCGTATTAATATATTGACATGTTA
Found at i:2369 original size:45 final size:45
Alignment explanation
Indices: 2302--2438 Score: 130
Period size: 45 Copynumber: 3.0 Consensus size: 45
2292 GCATAGCTCA
* * * *
2302 TCAAGCCAAGGATATCAGCCTCAGTTTGATGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAACCTCAATTTGACGAGCCACCACAATAC
* * * *
2347 TCAAGCCAATGATTTTAACCTCAATTTGACGAGCCACCATAATAC
1 TCAAGCCAAGGATATCAACCTCAATTTGACGAGCCACCACAATAC
** ** * * * *
2392 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCACCGCGATAC
1 TCAAGCCAAGGATATCAACCTCAATTTGACGAGCCACCACAATAC
2437 TC
1 TC
2439 TATTCCTCCC
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAACCTCAATTTGACGAGCCACCACAATAC
Found at i:2711 original size:14 final size:13
Alignment explanation
Indices: 2687--2760 Score: 67
Period size: 14 Copynumber: 5.4 Consensus size: 13
2677 TTCATAACAT
*
2687 TAAACCTTAAAACC
1 TAAA-CTTAAACCC
*
2701 TAAATTGTAAACCC
1 TAAACT-TAAACCC
2715 TAAACTTAAACCC
1 TAAACTTAAACCC
**
2728 TAAACTATAAATAC
1 TAAACT-TAAACCC
*
2742 TAAACTTGAAACTC
1 TAAACTT-AAACCC
2756 TAAAC
1 TAAAC
2761 CGTAAACACT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
13 15 0.30
14 35 0.70
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (13 bp):
TAAACTTAAACCC
Found at i:2724 original size:27 final size:27
Alignment explanation
Indices: 2682--2771 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
2672 TAAATTTCAT
* * *
2682 AACATTAAACCTTAAAACCTAAATTGTA
1 AACACTAAA-CTTAAAACCTAAACTATA
* *
2710 AACCCTAAACTTAAACCCTAAACTATA
1 AACACTAAACTTAAAACCTAAACTATA
* * **
2737 AATACTAAACTTGAAACTCTAAACCGTA
1 AACACTAAACTTAAAAC-CTAAACTATA
2765 AACACTA
1 AACACTA
2772 GATTGATTAA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
27 28 0.57
28 21 0.43
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.24
Consensus pattern (27 bp):
AACACTAAACTTAAAACCTAAACTATA
Found at i:6077 original size:4 final size:4
Alignment explanation
Indices: 6054--6105 Score: 77
Period size: 4 Copynumber: 12.8 Consensus size: 4
6044 TATCCTCTCC
* *
6054 TTCT TCCT TTCT TCCT TTCT TTCT TTCT TTCT TTCTT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTCT
6103 TTC
1 TTC
6106 CCGTTTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
4 39 0.91
5 4 0.09
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:12284 original size:16 final size:16
Alignment explanation
Indices: 12265--12318 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
12255 AAATTTAATG
12265 ATAAACAAATAAATAA
1 ATAAACAAATAAATAA
*
12281 ATAAACAAGATAATAAAA
1 ATAAACAA-ATAA-ATAA
12299 ATAAATACAAATTAAATAA
1 AT-AA-ACAAA-TAAATAA
12318 A
1 A
12319 AAATAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 8 0.26
17 4 0.13
18 5 0.16
19 7 0.23
20 7 0.23
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (16 bp):
ATAAACAAATAAATAA
Found at i:12326 original size:21 final size:21
Alignment explanation
Indices: 12271--12331 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
12261 AATGATAAAC
12271 AAATAAATAAATAA-ACAAGAT
1 AAATAAA-AAATAATACAAGAT
12292 -AAT-AAAAATAAATACAA-ATT
1 AAATAAAAAAT-AATACAAGA-T
*
12312 AAATAAAAAATAATAAAAGA
1 AAATAAAAAATAATACAAGA
12332 GATAACAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
18 4 0.12
19 5 0.15
20 8 0.24
21 9 0.27
22 7 0.21
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATAAAAAATAATACAAGAT
Found at i:12473 original size:16 final size:16
Alignment explanation
Indices: 12438--12480 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
12428 ATTGGGCATG
*
12438 AAAATAAA-AGACAAA
1 AAAATAAATAAACAAA
*
12453 TAAATAAATAAACAAA
1 AAAATAAATAAACAAA
*
12469 AAAATCAATAAA
1 AAAATAAATAAA
12481 TTAAATGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:13533 original size:97 final size:98
Alignment explanation
Indices: 13388--13581 Score: 237
Period size: 97 Copynumber: 2.0 Consensus size: 98
13378 TGTAAGATTC
* * * * * * * * *
13388 GCCGTTGTGGCTTCAATTTGTTCCCTCTTTGGTTTTAAGGTGTTAGATCTATCGTCATGACTTCA
1 GCCGTCGTGGCTTCAACTTGATCCCTCTTCGATTTTAAAGTGTAAGATCCATCATCATGACTTCA
* *
13453 ATCTATCCTTATTTGGTTTTAGGGTATTAGGTT
66 ATCTATCCATATTTGATTTTAGGGTATTAGGTT
* **
13486 GCCGTCGTGGCTTCAACTT-ATCCCTCTTCGATTTTAAAGTGTAAGATCCGTCATTGTGACTTCA
1 GCCGTCGTGGCTTCAACTTGATCCCTCTTCGATTTTAAAGTGTAAGATCCATCATCATGACTTCA
* *
13550 ATCTTTCCATATTTGATTTTAGGGTGTTAGGT
66 ATCTATCCATATTTGATTTTAGGGTATTAGGT
13582 CCGTCATTAC
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
97 63 0.79
98 17 0.21
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (98 bp):
GCCGTCGTGGCTTCAACTTGATCCCTCTTCGATTTTAAAGTGTAAGATCCATCATCATGACTTCA
ATCTATCCATATTTGATTTTAGGGTATTAGGTT
Found at i:13618 original size:49 final size:49
Alignment explanation
Indices: 13496--14251 Score: 408
Period size: 49 Copynumber: 15.4 Consensus size: 49
13486 GCCGTCGTGG
* * * * * * **
13496 CTTCAACTTATCCCTCTTCGATTTTAAAGTGTAAGATCCGTCATTGTGA
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * * * ** * *
13545 CTTCAATCTTTCCATATTTGATTTTAGGGTGTTAGGTCCGTCATTACGA
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * * * * * *
13594 GTTCAACCTATCCCTCTTCAATTTTAAGGTATAATGTTCATCGTTACGG
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * * * * * * * *
13643 CTTCAACCTTTCCCTCTTTAGTTTTAGGGTGTTAGATTCATCGTTAAGG
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
** * ** *
13692 CTTCAATTTATCCCTTTTTGATTTTAAGGTGTTAGGTTCGTCGTTACGA
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * * * * * *
13741 CTTTAACCTATCCCTCTTCGATTTTAAGGTGTAAGATCCCTCGTTGCAA
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * * * * * * *
13790 CTTCAATCTTTTCCTTTTCGATTTTTAGGTGTTAGATCCATCGTTACGA
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * * * *
13839 CTTCAACCTATCCCTCTTTAGTTTTAAGGTGTAAGGTCCGCCATTACGA
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * ** ** * **
13888 CTTTAACCTTTCCCTCTTCAATTTTAAGGTGTTAAATCCACCATTGTGA
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * * * ** * *
13937 CTTCAATCTATCCCTATTCGATTTT-AGGTTGTTAGATCCACCATTATGA
1 CTTCAACCTATCCCTCTTCAATTTTAAGG-TGTTAGGTCCGTCGTTACGA
** * * * * *
13986 CTTCAATTTATCCCTCTTCGATTTTAAAGTTTTAAGTTCGTCGTTACGA
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * * * * *
14035 CTTCAACTTATCCCTCTTCGATTTTAAGGTGTAAGATCCGCCGTTACGG
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* ** * ** * * * *** *
14084 CTTAAATTTTTCCCTCTTTGATTTTAGGGTCTTAAGTCTACCGTTACGG
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
* * *
14133 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGGTTGGCCGTTG-TA-G-
1 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGG-T--CCGTCGTTACGA
* * * * * * *
14182 CTTCAACCTTTCCATCTTCAGTTTT-AGGATATTAGGTCCG-CTATTGCGG
1 CTTCAACCTATCCCTCTTCAATTTTAAGG-TGTTAGGTCCGTC-GTTACGA
*
14231 CTTCAACCTATCCTTCTTCAA
1 CTTCAACCTATCCCTCTTCAA
14252 AATCTATGAT
Statistics
Matches: 542, Mismatches: 155, Indels: 20
0.76 0.22 0.03
Matches are distributed among these distances:
46 3 0.01
47 1 0.00
48 8 0.01
49 522 0.96
50 4 0.01
51 2 0.00
52 2 0.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (49 bp):
CTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTACGA
Found at i:13657 original size:147 final size:146
Alignment explanation
Indices: 13494--14109 Score: 526
Period size: 147 Copynumber: 4.2 Consensus size: 146
13484 TTGCCGTCGT
* * * * ** *
13494 GGCTTCAACTTATCCCTCTTCGATTTTAAAGTGTAAGATCCGTCATTGTGACTTCAATCTTTCCA
1 GGCTTCAACTT-TCCCTCTTCGATTTTAAGGTGTTAGATCCATCGTTAAGACTTCAATCTTTCCC
* * *
13559 TATTTGATTTTAGGGTGTTAGGTCCGTCATTACGAGTTCAACCTATCCCTCTTCAATTTTAAGGT
65 TATTTGATTTTAAGGTGTTAGGTCCGTCATTACGACTTTAACCTATCCCTCTTCAATTTTAAGGT
*
13624 ATAATG-TTCATCGTTAC
130 ATAA-GATCCATCGTTAC
* * * *
13641 GGCTTCAACCTTTCCCTCTT-TAGTTTTAGGGTGTTAGATTCATCGTTAAGGCTTCAAT-TTATC
1 GGCTTCAA-CTTTCCCTCTTCGA-TTTTAAGGTGTTAGATCCATCGTTAAGACTTCAATCTT-TC
* * * *
13704 CCTTTTTGATTTTAAGGTGTTAGGTTCGTCGTTACGACTTTAACCTATCCCTCTTCGATTTTAAG
63 CCTATTTGATTTTAAGGTGTTAGGTCCGTCATTACGACTTTAACCTATCCCTCTTCAATTTTAAG
* * *
13769 GTGTAAGATCCCTCGTTGC
128 GTATAAGATCCATCGTTAC
** * * * * * *
13788 AACTTCAATCTTTTCCTTTTCGATTTTTAGGTGTTAGATCCATCGTTACGACTTCAACCTATCCC
1 GGCTTCAA-CTTTCCCTCTTCGATTTTAAGGTGTTAGATCCATCGTTAAGACTTCAATCTTTCCC
* * * *
13853 TCTTT-AGTTTTAAGGTGTAAGGTCCGCCATTACGACTTTAACCTTTCCCTCTTCAATTTTAAGG
65 TATTTGA-TTTTAAGGTGTTAGGTCCGTCATTACGACTTTAACCTATCCCTCTTCAATTTTAAGG
* * * **
13917 TGTTAA-ATCCACCATTGT
129 T-ATAAGATCCATCGTTAC
* * * * * *
13935 GACTTCAATCTATCCCTATTCGATTTT-AGGTTGTTAGATCCACCATTATGACTTCAAT-TTATC
1 GGCTTCAA-CTTTCCCTCTTCGATTTTAAGG-TGTTAGATCCATCGTTAAGACTTCAATCTT-TC
* * * * * * * * * *
13998 CCTCTTCGATTTTAAAGTTTTAAGTTCGTCGTTACGACTTCAACTTATCCCTCTTCGATTTTAAG
63 CCTATTTGATTTTAAGGTGTTAGGTCCGTCATTACGACTTTAACCTATCCCTCTTCAATTTTAAG
* **
14063 GTGTAAGATCCGCCGTTAC
128 GTATAAGATCCATCGTTAC
* * *
14082 GGCTTAAATTTTTCCCTCTTTGATTTTA
1 GGCTTCAA-CTTTCCCTCTTCGATTTTA
14110 GGGTCTTAAG
Statistics
Matches: 377, Mismatches: 79, Indels: 25
0.78 0.16 0.05
Matches are distributed among these distances:
146 12 0.03
147 356 0.94
148 9 0.02
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (146 bp):
GGCTTCAACTTTCCCTCTTCGATTTTAAGGTGTTAGATCCATCGTTAAGACTTCAATCTTTCCCT
ATTTGATTTTAAGGTGTTAGGTCCGTCATTACGACTTTAACCTATCCCTCTTCAATTTTAAGGTA
TAAGATCCATCGTTAC
Found at i:14186 original size:147 final size:149
Alignment explanation
Indices: 13564--14207 Score: 564
Period size: 147 Copynumber: 4.4 Consensus size: 149
13554 TTCCATATTT
* * * * * * *
13564 GATTTTAGGGTGTTAGGTCCGTCATTACGAGTTCAACCTATCCCTCTTCAATTTTAAGGTATAAT
1 GATTTTAAGGTGTAAGGTTCGCCGTTACGACTTCAACCTATCCCTCTTCAATTTTAAGGTGTAA-
* * * * * * * *
13629 G-TTCATCGTTACGGCTTCAACCTTTCCCTCTTT-AGTTTTAGGGTGTTAGATTCATCGTTAAGG
65 GATCCACCGTTACGACTTCAATCTTTCCCTCTTTGAGTTTTAGGGTGTTAGATCCACCGTTACGA
** **
13692 CTTCAATTTATCCCT-TTTT
130 CTTCAACCTATCCCTCTTCA
* * * *
13711 GATTTTAAGGTGTTAGGTTCGTCGTTACGACTTTAACCTATCCCTCTTCGATTTTAAGGTGTAAG
1 GATTTTAAGGTGTAAGGTTCGCCGTTACGACTTCAACCTATCCCTCTTCAATTTTAAGGTGTAAG
* * * * *
13776 ATCC-CTCGTTGCAACTTCAATCTTTTCCT-TTTCGATTTTTA-GGTGTTAGATCCATCGTTACG
66 ATCCAC-CGTTACGACTTCAATCTTTCCCTCTTT-GAGTTTTAGGGTGTTAGATCCACCGTTACG
*
13838 ACTTCAACCTATCCCTCTTTA
129 ACTTCAACCTATCCCTCTTCA
* * * *
13859 G-TTTTAAGGTGTAAGGTCCGCCATTACGACTTTAACCTTTCCCTCTTCAATTTTAAGGTGTTAA
1 GATTTTAAGGTGTAAGGTTCGCCGTTACGACTTCAACCTATCCCTCTTCAATTTTAAGGTG-TAA
* ** * * * * * *
13923 -ATCCACCATTGTGACTTCAATCTATCCCTATTCGA-TTTTAGGTTGTTAGATCCACCATTATGA
65 GATCCACCGTTACGACTTCAATCTTTCCCTCTTTGAGTTTTAGGGTGTTAGATCCACCGTTACGA
**
13986 CTTCAATTTATCCCTCTTC-
130 CTTCAACCTATCCCTCTTCA
* * * * *
14005 GATTTTAAAGTTTTAA-GTTCGTCGTTACGACTTCAACTTATCCCTCTTCGATTTTAAGGTGTAA
1 GATTTT-AAGGTGTAAGGTTCGCCGTTACGACTTCAACCTATCCCTCTTCAATTTTAAGGTGTAA
* * * * * *
14069 GATCCGCCGTTACGGCTTAAATTTTTCCCTCTTTGA-TTTTAGGGTCTTA-AGTCTACCGTTACG
65 GATCCACCGTTACGACTTCAATCTTTCCCTCTTTGAGTTTTAGGGTGTTAGA-TCCACCGTTACG
*
14132 GCTTCAACCTATCCCTCTTCA
129 ACTTCAACCTATCCCTCTTCA
* * * *
14153 G-TTTTAAGGTGTAAGGTTGGCCGTT--GTAGCTTCAACCTTTCCATCTTCAGTTTTA
1 GATTTTAAGGTGTAAGGTTCGCCGTTACG-A-CTTCAACCTATCCCTCTTCAATTTTA
14208 GGATATTAGG
Statistics
Matches: 404, Mismatches: 76, Indels: 34
0.79 0.15 0.07
Matches are distributed among these distances:
145 1 0.00
146 22 0.05
147 357 0.88
148 24 0.06
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (149 bp):
GATTTTAAGGTGTAAGGTTCGCCGTTACGACTTCAACCTATCCCTCTTCAATTTTAAGGTGTAAG
ATCCACCGTTACGACTTCAATCTTTCCCTCTTTGAGTTTTAGGGTGTTAGATCCACCGTTACGAC
TTCAACCTATCCCTCTTCA
Found at i:15260 original size:13 final size:13
Alignment explanation
Indices: 15234--15275 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
15224 CCCCTATTTT
15234 TTTTGTTTTCTTCTC
1 TTTT-TTTT-TTCTC
15249 TTTTTTTTTTCT-
1 TTTTTTTTTTCTC
15261 TTTTTCTTTTTCTC
1 TTTTT-TTTTTCTC
15275 T
1 T
15276 CATTTTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.20
13 11 0.44
14 5 0.20
15 4 0.16
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTTCTC
Found at i:15267 original size:20 final size:20
Alignment explanation
Indices: 15230--15271 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
15220 TTGACCCCTA
*
15230 TTTTTTTTGTTTTCTTCTCTT
1 TTTTTTTTCTTTTCTTCT-TT
15251 TTTTTTTTCTTTT-TTCTTT
1 TTTTTTTTCTTTTCTTCTTT
15270 TT
1 TT
15272 CTCTCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (20 bp):
TTTTTTTTCTTTTCTTCTTT
Found at i:22059 original size:195 final size:195
Alignment explanation
Indices: 21726--22369 Score: 819
Period size: 195 Copynumber: 3.3 Consensus size: 195
21716 GAAACCGACG
* * * * * * *
21726 CGATGGCTAGGGTACTGCATATGTTGCGAG-CCTCAATAGCTCGTGTGAGTAGCATTGTGAGTCA
1 CGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCG
* * * * *
21790 GGAAAATGAGAAATGAATCCCATAGTGGATTACAGGCCTTATGATGGCTAAGATTTATGCATAAG
66 GGAAAATGAGAAATGAATCCAATAATGGATTACAAGCCCTAAGATGGCT-AGATTTATGCATAAG
* * *
21855 TGTATATTCTCGACAGCTCATGTGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTA
130 TGCATATTCTCGATAGCTCATATGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTA
21920 T
195 T
* ** * *
21921 CGATGGCTGAAGTACCGCACATGTTGCGAGTCCTCGATAGCTCGTATGAGCAGCATCGTGAGTCG
1 CGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCG
* * *
21986 GGAAAATGAGAAATG-ATCCAAGAATGGATTACAAGCCCTACGATGGTTGAGATTTATGCATAAG
66 GGAAAATGAGAAATGAATCCAATAATGGATTACAAGCCCTAAGATGGCT-AGATTTATGCATAAG
* * *
22050 CGCATATTCTCGATAGCTCATATGAGTAGCATCGTTAGGGAACAATTATATGCACAGATACCATA
130 TGCATATTCTCGATAGCTCATATGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTA
22115 T
195 T
** * * **
22116 CGATGGTTGGGGTACAACATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAATATCGTGAGTCG
1 CGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCG
* * * *
22181 AGAAAATGAGAAATGAATCTAATAATGGATTACATGCCCTAAGATGGCTAGGATTTATGAATAAG
66 GGAAAATGAGAAATGAATCCAATAATGGATTACAAGCCCTAAGATGGCTA-GATTTATGCATAAG
* * * * * *
22246 TGCATATTCTTGATAGCTCGTATGAGCAGCATCATTAGGGAACAGTTATAT-CATAGATATCGTA
130 TGCATATTCTCGATAGCTCATATGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTA
22310 T
195 T
* * *
22311 CGATGATTGGGGTACCGCATATGTTGTGAGTCCTCG-TCAGCTCGTGTGAACAGCATCGT
1 CGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGAT-AGCTCGTGTGAGCAGCATCGT
22370 ATACTGGTAG
Statistics
Matches: 385, Mismatches: 60, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
195 255 0.66
196 130 0.34
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (195 bp):
CGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCG
GGAAAATGAGAAATGAATCCAATAATGGATTACAAGCCCTAAGATGGCTAGATTTATGCATAAGT
GCATATTCTCGATAGCTCATATGAGCAGCATCGTTAGGGAACAATTATATGCACAGATACCGTAT
Found at i:28825 original size:18 final size:18
Alignment explanation
Indices: 28794--28828 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28784 AGTTAATTTT
*
28794 TTAATTCGGGTAATTCGA
1 TTAATTCGAGTAATTCGA
*
28812 TTAATTCGATTAATTCG
1 TTAATTCGAGTAATTCG
28829 GGTAATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (18 bp):
TTAATTCGAGTAATTCGA
Found at i:31018 original size:42 final size:42
Alignment explanation
Indices: 30898--31079 Score: 211
Period size: 42 Copynumber: 4.3 Consensus size: 42
30888 ACTTGGCGTA
* * *
30898 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGGTTATGTT
1 TAAA-GGAAGACTCGTGACTCGAGATGAGCATGAGATTATGTT
* * *
30941 TAAAAGGAAGACTTGTGACTCGAAAAGAGCATGAGATTATGTT
1 T-AAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATGTT
* * ** *
30984 TAAAGGAAGACTCGTGATTCGGGATGAGTGTGAGATTATATT
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATGTT
* * * *
31026 TAAAGGAAGACTCGTGACACGGGATCAGTATGAGATTATGTT
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATGTT
31068 TAAAGGAAGACT
1 TAAAGGAAGACT
31080 TATAACTTGG
Statistics
Matches: 119, Mismatches: 19, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
42 82 0.69
43 34 0.29
44 3 0.03
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (42 bp):
TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATGTT
Found at i:35495 original size:2 final size:2
Alignment explanation
Indices: 35488--35515 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35478 AACAAATAAA
35488 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
35516 CGAGGGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40726 original size:11 final size:11
Alignment explanation
Indices: 40710--40744 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40700 CATCATTTAA
40710 TTTTAAAATTT
1 TTTTAAAATTT
*
40721 TTTTAAAATTA
1 TTTTAAAATTT
*
40732 TTTGAAAATTT
1 TTTTAAAATTT
40743 TT
1 TT
40745 ATCCAAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:43107 original size:19 final size:20
Alignment explanation
Indices: 43061--43127 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 20
43051 TTTGTTAATT
43061 TTTTTAAAAATATACATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTG-AA
*
43085 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
43104 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
43123 TTTTT
1 TTTTT
43128 GTTGAGAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 8 0.21
19 11 0.28
20 10 0.26
22 1 0.03
24 9 0.23
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:43980 original size:8 final size:9
Alignment explanation
Indices: 43959--44001 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
43949 ATTAAAATAT
43959 TTTTTATAA
1 TTTTTATAA
43968 TTTTT-TAA
1 TTTTTATAA
*
43976 TTTTTAAAA
1 TTTTTATAA
43985 TAGTTTTATAA
1 T--TTTTATAA
43996 TTTTTA
1 TTTTTA
44002 AAAAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 8 0.28
9 13 0.45
11 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:44518 original size:19 final size:21
Alignment explanation
Indices: 44495--44542 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
44485 TATATATTTT
44495 TAAAAAATTATAATAAAT-TA
1 TAAAAAATTATAATAAATATA
* *
44515 -AAAAAATTCTAATGAATATA
1 TAAAAAATTATAATAAATATA
44535 TAAAAAAT
1 TAAAAAAT
44543 CAAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 15 0.62
20 2 0.08
21 7 0.29
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAAAAATTATAATAAATATA
Found at i:53677 original size:28 final size:28
Alignment explanation
Indices: 53630--53683 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
53620 TTTGCATACT
* *
53630 TGTATTTTTTGAACATATTGGTTTAACC
1 TGTATTTTTTGAACAAATTGATTTAACC
*
53658 TGTATTTTTTGGACAAATTGATTTAA
1 TGTATTTTTTGAACAAATTGATTTAA
53684 TAATAGCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (28 bp):
TGTATTTTTTGAACAAATTGATTTAACC
Found at i:56694 original size:36 final size:34
Alignment explanation
Indices: 56614--56706 Score: 96
Period size: 36 Copynumber: 2.7 Consensus size: 34
56604 GTCACATTAT
** * *
56614 CAGAAACATATATAAGATTAGAATGTTATATTTC
1 CAGAAACATATACCATATCAGAATGTTATATTTC
* *
56648 CAGAAGCATATACCATATCAGAATGTATCATATTTT
1 CAGAAACATATACCATATCAGAATGT-T-ATATTTC
* *
56684 CATAAACATATATCATATCAGAA
1 CAGAAACATATACCATATCAGAA
56707 CAAATCCTGC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
34 21 0.44
35 1 0.02
36 26 0.54
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (34 bp):
CAGAAACATATACCATATCAGAATGTTATATTTC
Found at i:63653 original size:82 final size:82
Alignment explanation
Indices: 63253--63655 Score: 493
Period size: 82 Copynumber: 4.9 Consensus size: 82
63243 ACAAATTCCT
* * * * * * * *
63253 TCAATTCATGGCACCCAGAGCCTAGCGGATAAATCATAGTAAATGAGCCCAGTTCTAGTTAGATT
1 TCAATTCATGACACCCAGTGCCTAGCGGATAAACCACAATAAGTGAGCCCAGCTCTAGTTGGATT
*
63318 AACCAACAATAGTTTCG
66 AACCAACGATAGTTTCG
* * * * ** *
63335 TTAATTCATGGCACCCAGTGCTTAGCGAATAAACTGCAATAAGTGAGCTCAGCTCTAGTTGGATT
1 TCAATTCATGACACCCAGTGCCTAGCGGATAAACCACAATAAGTGAGCCCAGCTCTAGTTGGATT
63400 AACCAACGATAGTTTCG
66 AACCAACGATAGTTTCG
* * * * * *
63417 TCAATTCCT-AGCACCTAGTGCCTACCAGATAAACCGCAATAAGTGAGCTCAGCTCTAGTTGGAT
1 TCAATTCATGA-CACCCAGTGCCTAGCGGATAAACCACAATAAGTGAGCCCAGCTCTAGTTGGAT
* *
63481 TAACCAACAATAGTTTCA
65 TAACCAACGATAGTTTCG
* * * * *
63499 TCAATTCCTAACACCTAGTGCCTAGCGAATAAACCACAATAAGTGAGCCCAGCTTTAGTTGGATT
1 TCAATTCATGACACCCAGTGCCTAGCGGATAAACCACAATAAGTGAGCCCAGCTCTAGTTGGATT
*
63564 AACCAACGATAGTTTTG
66 AACCAACGATAGTTTCG
* * *
63581 TCAATTCTTGACACCCAGTGCCTAACGGATAAACCATAATAAGTGAGCCCAGCTCTAGTTGGATT
1 TCAATTCATGACACCCAGTGCCTAGCGGATAAACCACAATAAGTGAGCCCAGCTCTAGTTGGATT
63646 AACCAACGAT
66 AACCAACGAT
63656 TTTGCACGCA
Statistics
Matches: 278, Mismatches: 41, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
82 277 1.00
83 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (82 bp):
TCAATTCATGACACCCAGTGCCTAGCGGATAAACCACAATAAGTGAGCCCAGCTCTAGTTGGATT
AACCAACGATAGTTTCG
Found at i:64627 original size:3 final size:3
Alignment explanation
Indices: 64619--64645 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
64609 CGGTTCACCC
64619 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
64646 TTTTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:77011 original size:15 final size:15
Alignment explanation
Indices: 76991--77020 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
76981 AGACATTATC
76991 AAAAGGACGTTTTCA
1 AAAAGGACGTTTTCA
77006 AAAAGGACGTTTTCA
1 AAAAGGACGTTTTCA
77021 GAACATCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
AAAAGGACGTTTTCA
Found at i:77579 original size:24 final size:24
Alignment explanation
Indices: 77552--77598 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
77542 ATTTTCAAAA
*
77552 GTTTA-TAAATATGAATATAAATAT
1 GTTTATTAAAAAT-AATATAAATAT
*
77576 GTTTATTAAAAATAATCTAAATA
1 GTTTATTAAAAATAATATAAATA
77599 AAATCTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (24 bp):
GTTTATTAAAAATAATATAAATAT
Found at i:80973 original size:15 final size:16
Alignment explanation
Indices: 80955--80984 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
80945 AAATATAATT
80955 TTTTCT-TTTTTTTTC
1 TTTTCTCTTTTTTTTC
80970 TTTTCTCTTTTTTTT
1 TTTTCTCTTTTTTTT
80985 TTCTTATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTCTCTTTTTTTTC
Found at i:80978 original size:17 final size:17
Alignment explanation
Indices: 80953--80985 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
80943 GCAAATATAA
*
80953 TTTTTTCTTTTTTTTTC
1 TTTTCTCTTTTTTTTTC
80970 TTTTCTCTTTTTTTTT
1 TTTTCTCTTTTTTTTT
80986 TCTTATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTCTCTTTTTTTTTC
Found at i:84526 original size:107 final size:107
Alignment explanation
Indices: 84340--84549 Score: 357
Period size: 107 Copynumber: 2.0 Consensus size: 107
84330 TCGGCAGCAT
* * *
84340 CATAGTCTATATTCACCTGCTTGATTGCCTACATGGCCTTATGTTTAAGCTTAAATAGCAGGTGA
1 CATAGTCTATATTCACCTGCTTGATTGCCCACATGGCCTTATGTTCAAGCTTAAATAGCACGTGA
84405 CAAGACTTACCAAACAATAATTGATATGGCGACATTCCCAAC
66 CAAGACTTACCAAACAATAATTGATATGGCGACATTCCCAAC
* *
84447 CATAGTCTATATTCACTTGCTTGATTGCCCACATGGCCTTATGTTCAAGCTTAACTAGCACGTGA
1 CATAGTCTATATTCACCTGCTTGATTGCCCACATGGCCTTATGTTCAAGCTTAAATAGCACGTGA
* *
84512 CAAGACTTATCAAACACTAATTGATATGGCGACATTCC
66 CAAGACTTACCAAACAATAATTGATATGGCGACATTCC
84550 TAACGGGGTC
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 96 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (107 bp):
CATAGTCTATATTCACCTGCTTGATTGCCCACATGGCCTTATGTTCAAGCTTAAATAGCACGTGA
CAAGACTTACCAAACAATAATTGATATGGCGACATTCCCAAC
Done.