Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016531.1 Corchorus olitorius cultivar O-4 contig16564, 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: 93481
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8339 original size:85 final size:85
Alignment explanation
Indices: 8239--8408 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
8229 GTATATAATA
*
8239 TATATATATATAAGAAAATATGAAAAAAAAAAGAGATACAAAAATTTGAAATCAATCATCATTTG
1 TATATATATATAAGAAAATATGAAAAAAAAAAGAAATACAAAAATTTGAAATCAATCATCATTTG
8304 TTAATGGATCATAAAAAGGT
66 TTAATGGATCATAAAAAGGT
8324 TATATATATATAAGAAAATATGAAAAAAAAAAGAAATACAAAAATTTGAAATCAATCATCATTTG
1 TATATATATATAAGAAAATATGAAAAAAAAAAGAAATACAAAAATTTGAAATCAATCATCATTTG
8389 TTAATGGATCATAAAAAGGT
66 TTAATGGATCATAAAAAGGT
8409 AGAGGCGTAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (85 bp):
TATATATATATAAGAAAATATGAAAAAAAAAAGAAATACAAAAATTTGAAATCAATCATCATTTG
TTAATGGATCATAAAAAGGT
Found at i:16129 original size:19 final size:18
Alignment explanation
Indices: 16101--16140 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
16091 TACTAATTAA
16101 TTATTTTATATTAAATTT
1 TTATTTTATATTAAATTT
*
16119 TTATTTATATATTATATTT
1 TTATTT-TATATTAAATTT
16138 TTA
1 TTA
16141 CTTAAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTTATATTAAATTT
Found at i:20076 original size:32 final size:32
Alignment explanation
Indices: 20035--20095 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
20025 AAATATGTTT
20035 GAAAAATAAGGGTATAAT-GATCGATTCAATTA
1 GAAAAATAAGGGTATAATAG-TCGATTCAATTA
20067 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGGTATAATAGTCGATTCAA
20096 AAGTTTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGGTATAATAGTCGATTCAATTA
Found at i:21352 original size:22 final size:21
Alignment explanation
Indices: 21296--21448 Score: 153
Period size: 22 Copynumber: 7.0 Consensus size: 21
21286 GTCTCTGTAT
*
21296 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
21317 TGATTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
21340 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
21362 GCTTATCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
21384 AGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
*
21406 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
21428 GGTTACCAAAATTTCATAGGA
1 GGTTATCAAAATTTCATAGGA
21449 TCAGGTTATT
Statistics
Matches: 106, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
21 5 0.05
22 96 0.91
23 5 0.05
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:21409 original size:66 final size:66
Alignment explanation
Indices: 21298--21445 Score: 201
Period size: 66 Copynumber: 2.2 Consensus size: 66
21288 CTCTGTATGG
* * *
21298 TTATCAAAATTTCATAAGATGATTATTATAATTTCATGAGGAGGTTATCAAAATTCCATAGTGTG
1 TTATCAAAATTTCATAAGAAGATTATCAAAATTTCATGAGGAGGTTATCAAAATTCCATAGTGTG
21363 C
66 C
* *
21364 TTATCAAAATTTCATATGGAAG-TTATCAAAATTTCATG-GGAAGGTTATCAAAATTTCATAGTG
1 TTATCAAAATTTCATA-AGAAGATTATCAAAATTTCATGAGG-AGGTTATCAAAATTCCATAGTG
*
21427 TGG
64 TGC
*
21430 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
21446 GGATCAGGTT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.03
66 68 0.93
67 3 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (66 bp):
TTATCAAAATTTCATAAGAAGATTATCAAAATTTCATGAGGAGGTTATCAAAATTCCATAGTGTG
C
Found at i:21537 original size:39 final size:39
Alignment explanation
Indices: 21487--21584 Score: 160
Period size: 39 Copynumber: 2.5 Consensus size: 39
21477 TGAAATTTTA
* *
21487 TAGTGTGGTTATCACAATTTTCTAGAATGTTTATCAAAG
1 TAGTGTGGTTATCACAATTTTCTAGAAAGGTTATCAAAG
21526 TAGTGTGGTTATCACAATTTTCTAGAAAGGTTATCAAAG
1 TAGTGTGGTTATCACAATTTTCTAGAAAGGTTATCAAAG
* *
21565 CAGTGTGGTTATCAAAATTT
1 TAGTGTGGTTATCACAATTT
21585 CATATGAAGG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (39 bp):
TAGTGTGGTTATCACAATTTTCTAGAAAGGTTATCAAAG
Found at i:21595 original size:39 final size:38
Alignment explanation
Indices: 21488--21603 Score: 153
Period size: 39 Copynumber: 3.0 Consensus size: 38
21478 GAAATTTTAT
* *
21488 AGTGTGGTTATCACAATTTTCTAGAATGTTTATCAAAGT
1 AGTGTGGTTATCACAATTTTCTAGAA-GGTTATCAAAGC
21527 AGTGTGGTTATCACAATTTTCTAGAAAGGTTATCAAAGC
1 AGTGTGGTTATCACAATTTTCTAG-AAGGTTATCAAAGC
* *
21566 AGTGTGGTTATCA-AAATTTCATATGAAGGTTATAAAAG
1 AGTGTGGTTATCACAATTTTC-TA-GAAGGTTATCAAAG
21604 TCTCAATTTC
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
38 6 0.09
39 61 0.87
40 3 0.04
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.36
Consensus pattern (38 bp):
AGTGTGGTTATCACAATTTTCTAGAAGGTTATCAAAGC
Found at i:21677 original size:22 final size:21
Alignment explanation
Indices: 21608--21792 Score: 94
Period size: 22 Copynumber: 8.5 Consensus size: 21
21598 TAAAAGTCTC
* *
21608 AATTTCATA-ATGAGTACCAA
1 AATTTCATAGATGATTATCAA
* * * *
21628 AAATTGATAGAGGGTTATC-A
1 AATTTCATAGATGATTATCAA
* *
21648 AATCTCATAGACTGATTATCGA
1 AATTTCATAGA-TGATTATCAA
21670 AATTTCATAGAGATTGAATTATCAA
1 AATTTCAT--AGA-TG-ATTATCAA
*
21695 AATTT-ATAGGAAGATTATCAA
1 AATTTCATA-GATGATTATCAA
*
21716 AATTTCATA-ATGTTGTTATCAA
1 AATTTCATAGATG--ATTATCAA
* **
21738 AATTTCAAAGCGA-GGCTATCAA
1 AATTTCATA--GATGATTATCAA
*
21760 AATTACATA-ATGTGATTATCAA
1 AATTTCATAGA--TGATTATCAA
21782 AATTTCATAGA
1 AATTTCATAGA
21793 GGGGCCAACA
Statistics
Matches: 124, Mismatches: 24, Indels: 31
0.69 0.13 0.17
Matches are distributed among these distances:
19 1 0.01
20 18 0.15
21 24 0.19
22 57 0.46
23 3 0.02
24 8 0.06
25 13 0.10
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (21 bp):
AATTTCATAGATGATTATCAA
Found at i:21805 original size:44 final size:44
Alignment explanation
Indices: 21687--21879 Score: 171
Period size: 44 Copynumber: 4.4 Consensus size: 44
21677 TAGAGATTGA
**
21687 ATTATCAAAATTT-ATAG-GAAGATTATCAAAATTTCATAATGTTG
1 ATTATCAAAATTTCATAGAG-AGGCTATCAAAATTTCATAATG-TG
* * *
21731 -TTATCAAAATTTCAAAGCGAGGCTATCAAAATTACATAATGTG
1 ATTATCAAAATTTCATAGAGAGGCTATCAAAATTTCATAATGTG
* * * * *
21774 ATTATCAAAATTTCATAGAGGGGCCAACAAAATTTTATAGA-GAG
1 ATTATCAAAATTTCATAGAGAGGCTATCAAAATTTCATA-ATGTG
* * * * *
21818 GTTATCAAAATTTCATAAAGAGGTTATC-AAATTTGCAAAATGCG
1 ATTATCAAAATTTCATAGAGAGGCTATCAAAATTT-CATAATGTG
*
21862 ATTACCAAAATTTCATAG
1 ATTATCAAAATTTCATAG
21880 TGGTACTTCT
Statistics
Matches: 119, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
43 21 0.18
44 96 0.81
45 2 0.02
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (44 bp):
ATTATCAAAATTTCATAGAGAGGCTATCAAAATTTCATAATGTG
Found at i:21841 original size:22 final size:22
Alignment explanation
Indices: 21688--21878 Score: 124
Period size: 22 Copynumber: 8.7 Consensus size: 22
21678 AGAGATTGAA
21688 TTATCAAAATTT-ATAGGAAGA--
1 TTATCAAAATTTCATA--AAGAGG
* **
21709 TTATCAAAATTTCATAATGTTG
1 TTATCAAAATTTCATAAAGAGG
*
21731 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * * * *
21753 CTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* *
21775 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
** * * *
21797 CCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAAAGAGG
21819 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
* *
21841 TTATC-AAATTTGCA-AAATGCGA
1 TTATCAAAATTT-CATAAA-GAGG
*
21863 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
21879 GTGGTACTTC
Statistics
Matches: 132, Mismatches: 29, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.02
21 23 0.17
22 98 0.74
23 9 0.07
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:22010 original size:22 final size:22
Alignment explanation
Indices: 21933--22364 Score: 207
Period size: 22 Copynumber: 19.9 Consensus size: 22
21923 CAAATTAGGA
* * *
21933 AGGTTATTAAACTTTTATTATGG
1 AGGTTATCAAAATTTCA-TATGG
* *
21956 A-GTAATCAAAATTTC--AGGG
1 AGGTTATCAAAATTTCATATGG
* * *
21975 AGGATAGCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGG
**
21997 AGGTTATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATA-TGG
* *
22020 A-GTTTTCAAAATTTCATA-AG
1 AGGTTATCAAAATTTCATATGG
*
22040 AGGATTATCAAAATTTCATA-GT
1 AGG-TTATCAAAATTTCATATGG
* * *
22062 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATATGG
* *
22085 AGATTAACAAAATTTCATAAT-G
1 AGGTTATCAAAATTTCAT-ATGG
** *
22107 AGGTTATCAAAAAATCATAGGG
1 AGGTTATCAAAATTTCATATGG
*
22129 AGGTTATCAAAA--T--T-TGT
1 AGGTTATCAAAATTTCATATGG
* *
22146 A-GTTATCAAGATTTCATAAGG
1 AGGTTATCAAAATTTCATATGG
* *
22167 AGGTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATATGG
*
22189 AGGTTTATCAAAATTTTATA-GG
1 AGG-TTATCAAAATTTCATATGG
* *
22211 AAGTTTTATCAAAATTTCAGA-GTG
1 -AG-GTTATCAAAATTTCATATG-G
**
22235 AAATTA-CTAACAA-TTCATATGG
1 AGGTTATC-AA-AATTTCATATGG
* * * **
22257 AGGTTTTTAAATTTTCATAACG
1 AGGTTATCAAAATTTCATATGG
* * * *
22279 TGATTATCAATATATCATATGG
1 AGGTTATCAAAATTTCATATGG
* * *
22301 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATA-TGG
*
22324 TGGTTATCAAAATTTCAT-TGG
1 AGGTTATCAAAATTTCATATGG
**
22345 AAAATTATCAAAATTTCATA
1 -AGGTTATCAAAATTTCATA
22365 GTGATGTCTT
Statistics
Matches: 306, Mismatches: 75, Indels: 56
0.70 0.17 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
19 4 0.01
20 14 0.05
21 9 0.03
22 204 0.67
23 61 0.20
24 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGG
Found at i:22037 original size:44 final size:43
Alignment explanation
Indices: 21982--22408 Score: 272
Period size: 44 Copynumber: 9.8 Consensus size: 43
21972 GGGAGGATAG
* * *
21982 CAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTT
1 CAAAATTTCATATGGAGGTTATCAAAATTTCATAG-TGAGTTAT
* *
22026 CAAAATTTCATA-AGAGGATTATCAAAATTTCATAGT-ATGTAGAT
1 CAAAATTTCATATGGAGG-TTATCAAAATTTCATAGTGA-GT-TAT
* * * *
22070 CAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTAT
1 CAAAATTTCATATGGAGGTTATCAAAATTTCATAGTGA-GTTAT
** *
22114 CAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GT-AGTTAT
1 CAAAATTTCATATGGAGGTTATCAAAATTTCATAGTGAGTTAT
* * * *
22152 CAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTTTAT
1 CAAAATTTCATATGGAGGTTATCAAAATTTCATAGTGA-G-TTAT
* * * *
22197 CAAAATTTTATA-GGAAGTTTTATCAAAATTTCAGAGTGAAATTA-
1 CAAAATTTCATATGG-AG-GTTATCAAAATTTCATAGTG-AGTTAT
* * *
22241 CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGTGA-TTAT
1 C-AA-AATTTCATATGGAGGTTATCAAAATTTCAT-A-GTGAGTTAT
* * * * *
22286 CAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGTTAT
1 CAAAATTTCATATGGAGGTTATCAAAATTTCATAGTG--AGTTAT
**
22331 CAAAATTTCAT-TGGAAAATTATCAAAATTTCATAGTGATGTCT-T
1 CAAAATTTCATATGG-AGGTTATCAAAATTTCATAGTGA-GT-TAT
* *
22375 CAAAA-TTCGGTA-GAGAGGTTAACAAAATTTCATA
1 CAAAATTTC-ATATG-GAGGTTATCAAAATTTCATA
22409 AGTTTAAACA
Statistics
Matches: 300, Mismatches: 52, Indels: 62
0.72 0.13 0.15
Matches are distributed among these distances:
38 28 0.09
39 3 0.01
40 1 0.00
41 2 0.01
42 5 0.02
43 14 0.05
44 153 0.51
45 70 0.23
46 23 0.08
47 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (43 bp):
CAAAATTTCATATGGAGGTTATCAAAATTTCATAGTGAGTTAT
Found at i:22138 original size:66 final size:66
Alignment explanation
Indices: 21982--22408 Score: 254
Period size: 66 Copynumber: 6.5 Consensus size: 66
21972 GGGAGGATAG
* * * ** *
21982 CAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG-TTTTCAAAATTTCATAA-GAGGAT
1 CAAAAATTCATAGGGAGGTTATCAAAATTTCATAG-GAAGATTATCAAAATTTCATAATGAGG-T
22045 TAT
64 TAT
* * * * * *
22048 CAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 CAAAAATTCATAGGGAGGT-TATCAAAATTTCATAGGAAGATTATCAAAATTTCATAATGAGGTT
22112 AT
65 AT
* * * *
22114 CAAAAAATCATAGGGAGGTTATCAAAA-TT--T--GTAG-TTATCAAGATTTCATAAGGAGGTTA
1 CAAAAATTCATAGGGAGGTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAATGAGGTTA
22173 T
66 T
* * * * * * **
22174 CAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGTTTTATCAAAATTTCAGAGTGAAAT
1 CAAAAATTCATAGGGAGG-TTATCAAAATTTCATAGGAAG-ATTATCAAAATTTCATAATGAGGT
22239 TA-
64 TAT
* * * * * * * * *
22241 CTAACAATTCATATGGAGGTTTTTAAATTTTCATAACG-TGATTATCAATATATCAT-ATGGAGG
1 C-AAAAATTCATAGGGAGGTTATCAAAATTTCAT-AGGAAGATTATCAAAATTTCATAAT-GAGG
22304 TTAT
63 TTAT
* ** * * * *
22308 C-AACATCTCATAGTGTTGGTTATCAAAATTTCATTGGAAAATTATCAAAATTTCATAGTGATGT
1 CAAAAAT-TCATAG-GGAGGTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAATGAGGT
22372 CT-T
64 -TAT
* * *
22375 C-AAAATTCGGTAGAGAGGTTAACAAAATTTCATA
1 CAAAAATTC-ATAGGGAGGTTATCAAAATTTCATA
22409 AGTTTAAACA
Statistics
Matches: 273, Mismatches: 66, Indels: 44
0.71 0.17 0.11
Matches are distributed among these distances:
60 38 0.14
61 12 0.04
62 2 0.01
63 1 0.00
64 1 0.00
65 12 0.04
66 107 0.39
67 64 0.23
68 36 0.13
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (66 bp):
CAAAAATTCATAGGGAGGTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAATGAGGTTA
T
Found at i:22200 original size:23 final size:23
Alignment explanation
Indices: 22148--22227 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
22138 AAATTTGTAG
* * *
22148 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
22170 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
22193 TTATCAAAATTTTATAGGAAGTT
1 TTATCAAAATTTTATAGGGAGGT
22216 TTATCAAAATTT
1 TTATCAAAATTT
22228 CAGAGTGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
22 19 0.37
23 33 0.63
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:23257 original size:12 final size:12
Alignment explanation
Indices: 23240--23264 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23230 TCATAATTAC
23240 AATAAATTGAGA
1 AATAAATTGAGA
23252 AATAAATTGAGA
1 AATAAATTGAGA
23264 A
1 A
23265 GAATGCTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
AATAAATTGAGA
Found at i:29557 original size:13 final size:13
Alignment explanation
Indices: 29539--29564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29529 AAGAATTCAA
29539 ATATATTTAATTG
1 ATATATTTAATTG
29552 ATATATTTAATTG
1 ATATATTTAATTG
29565 CGTTTTTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATATATTTAATTG
Found at i:29639 original size:43 final size:43
Alignment explanation
Indices: 29591--29676 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
29581 AACATCCGAC
*
29591 CTACAACCAATTGTTTATAGGTGGAGAGTCTCTTCATGTATAT
1 CTACAACCAATTGTTTATAGGTGGAGAGCCTCTTCATGTATAT
29634 CTACAACCAATTGTTTATAGGTGGAGAGCCTCTTCATGTATAT
1 CTACAACCAATTGTTTATAGGTGGAGAGCCTCTTCATGTATAT
29677 AAGGTTTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (43 bp):
CTACAACCAATTGTTTATAGGTGGAGAGCCTCTTCATGTATAT
Found at i:29689 original size:34 final size:34
Alignment explanation
Indices: 29646--29715 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
29636 ACAACCAATT
29646 GTTTATAGGTGGAGAGCCTCTTCATGTATATAAG
1 GTTTATAGGTGGAGAGCCTCTTCATGTATATAAG
*
29680 GTTTATAGGTGGAGAGGCTCTTCATGTATATAAG
1 GTTTATAGGTGGAGAGCCTCTTCATGTATATAAG
29714 GT
1 GT
29716 ACTCAGTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.36
Consensus pattern (34 bp):
GTTTATAGGTGGAGAGCCTCTTCATGTATATAAG
Found at i:30064 original size:196 final size:202
Alignment explanation
Indices: 29684--30174 Score: 672
Period size: 196 Copynumber: 2.4 Consensus size: 202
29674 TATAAGGTTT
*
29684 ATAGGTGGAGAGGCTCTTCATGTATATAAGGTACTCAGTCATGTCAAATATAACCAATGTGGGAT
1 ATAGGTGGAGAGGC-CTTCATGTATATAAGGTAC-CAGTCATGTCAAACATAACCAATGTGGGAT
*
29749 ATTACCACTTTAACACGCCCCCTCACGTGTAGCCCGGGACAACACCGAAACAGAACAGGCCTACA
64 ATTACCACTTTAACACGCCCCCTCACGTATAGCCCGGGACAACACCGAAACAGAACAGGCCTACA
* * * * * * * *
29814 CGTGGACACAACCGGGCCTGGGGCGCAATAGGATAGACTTGAGCTCTGATACCATGTTAAGCAT-
129 CATGGACACAACCGAGCCTGGGGCACAACAGGACAGACCTAAGCTCTAATACCATGTTAAGCATA
29878 CC-AA-C-C
194 CCAAACCAC
29884 -TAGGTGGAGAGG-CTTCATGTATATAAGGTATCCAGTCATGTCAAACATAACCAATGTGGGATA
1 ATAGGTGGAGAGGCCTTCATGTATATAAGGTA-CCAGTCATGTCAAACATAACCAATGTGGGATA
*
29947 TTACCACTTTAACACG-CCCCTCACGTATAGCCCGGGACAACACCGAAACAGAACGGGCCTACAC
65 TTACCACTTTAACACGCCCCCTCACGTATAGCCCGGGACAACACCGAAACAGAACAGGCCTACAC
*
30011 ATGGACACAACCGAGTCTGGGGCACAACAGGACAGACCTAAGCTCTAATACCATGTTAAGCATCC
130 ATGGACACAACCGAGCCTGGGGCACAACAGGACAGACCTAAGCTCTAATACCATGTTAAGCAT--
30076 AACCTAAAACCAATTGGC
193 -ACC--AAACC-A----C
*
30094 TATAGGTGGAGAGGCTCTTCATGTATATAAGGTACCCAGTCATGTCAAACATAACCAATGTAGGA
1 -ATAGGTGGAGAGGC-CTTCATGTATATAAGGTA-CCAGTCATGTCAAACATAACCAATGTGGGA
30159 TATTACCACTTTAACA
63 TATTACCACTTTAACA
30175 TCTATAATGT
Statistics
Matches: 258, Mismatches: 14, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
196 100 0.39
197 64 0.25
198 1 0.00
199 12 0.05
200 2 0.01
203 2 0.01
204 1 0.00
210 1 0.00
212 12 0.05
214 63 0.24
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (202 bp):
ATAGGTGGAGAGGCCTTCATGTATATAAGGTACCAGTCATGTCAAACATAACCAATGTGGGATAT
TACCACTTTAACACGCCCCCTCACGTATAGCCCGGGACAACACCGAAACAGAACAGGCCTACACA
TGGACACAACCGAGCCTGGGGCACAACAGGACAGACCTAAGCTCTAATACCATGTTAAGCATACC
AAACCAC
Found at i:35746 original size:31 final size:31
Alignment explanation
Indices: 35700--35778 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
35690 ATTTTTAGTC
*
35700 ACCAATTTGATGCTAAACCTTTCAAAAGTTG
1 ACCAATTTGAGGCTAAACCTTTCAAAAGTTG
* *
35731 -CTCAGTTTGAGGCTAAACTTTTCAAAAGTTG
1 AC-CAATTTGAGGCTAAACCTTTCAAAAGTTG
*
35762 ACCAATTTGAGTCTAAA
1 ACCAATTTGAGGCTAAA
35779 AAACAGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 39 0.95
32 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (31 bp):
ACCAATTTGAGGCTAAACCTTTCAAAAGTTG
Found at i:36173 original size:17 final size:16
Alignment explanation
Indices: 36133--36181 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
36123 CATGTAATCT
*
36133 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
36149 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
36166 TTAGATCACTAGTGAT
1 TT-GATCACTGGTGAT
36182 TTGGGGGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:40776 original size:31 final size:31
Alignment explanation
Indices: 40653--40779 Score: 123
Period size: 31 Copynumber: 4.2 Consensus size: 31
40643 TGACACGTGG
* * *
40653 CACGTGTC-CTTTTT-GTGCACGAGCCATGC
1 CACGTGTCGCTTTTTGGTACACGTGGCATGC
* * ** *
40682 CACGTGTCACTTTTTGGTACATGTGGTGTGA
1 CACGTGTCGCTTTTTGGTACACGTGGCATGC
* * * *
40713 CACATGTCGCTTTTTGATACATGTGGCGTGC
1 CACGTGTCGCTTTTTGGTACACGTGGCATGC
*
40744 CACGTGTCGCTTTTTGGTACACGTGGTATGC
1 CACGTGTCGCTTTTTGGTACACGTGGCATGC
40775 CACGT
1 CACGT
40780 CGGACACCGT
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
29 8 0.10
30 6 0.08
31 65 0.82
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.35
Consensus pattern (31 bp):
CACGTGTCGCTTTTTGGTACACGTGGCATGC
Found at i:46502 original size:29 final size:28
Alignment explanation
Indices: 46459--46513 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
46449 AATTTATACG
46459 ATTTTGATATTTTACCACCTAAACTTTA
1 ATTTTGATATTTTACCACCTAAACTTTA
* *
46487 ATTTTGGATGTTTTACCTCCTAAACTT
1 ATTTT-GATATTTTACCACCTAAACTT
46514 ACAATTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.47
Consensus pattern (28 bp):
ATTTTGATATTTTACCACCTAAACTTTA
Found at i:46521 original size:29 final size:29
Alignment explanation
Indices: 46459--46523 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
46449 AATTTATACG
*
46459 ATTTTGATATTTTACCACCTAAACTTTAA
1 ATTTGGATATTTTACCACCTAAACTTTAA
* * *
46488 TTTTGGATGTTTTACCTCCTAAAC-TTACA
1 ATTTGGATATTTTACCACCTAAACTTTA-A
46517 ATTTGGA
1 ATTTGGA
46524 GACACGTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (29 bp):
ATTTGGATATTTTACCACCTAAACTTTAA
Found at i:54752 original size:87 final size:86
Alignment explanation
Indices: 54655--54841 Score: 252
Period size: 84 Copynumber: 2.2 Consensus size: 86
54645 ACGTAAGGGA
* * * * *
54655 GGTGGAGGTGGTGGGGGAGGTCCTGATGCCTGAAGCTCTGGTGTAGAAGAACTTGTGCAGGTGGC
1 GGTGGAGG-GGTGGAGGAGGTCCTAATGCCTGAAGCTCAGGTGGAGAAGAAATTGTGCAGGTGGC
54720 TGAGGAAGAAATAGCAGGGAGT
65 TGAGGAAGAAATAGCAGGGAGT
* *
54742 GGTGGA--GGTGGAGGAGGTCCTAATGCCTGAAGGTCAGGTGGAGAAGAAATTGTGCAGGTGGTT
1 GGTGGAGGGGTGGAGGAGGTCCTAATGCCTGAAGCTCAGGTGGAGAAGAAATTGTGCAGGTGGCT
** *
54805 GAGGAAGTGATAGCAGGGGGT
66 GAGGAAGAAATAGCAGGGAGT
54826 GGTGGAGGAGGTGGAG
1 GGTGGAGG-GGTGGAG
54842 CTGAAAATGA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
84 74 0.85
87 13 0.15
ACGTcount: A:0.24, C:0.09, G:0.48, T:0.20
Consensus pattern (86 bp):
GGTGGAGGGGTGGAGGAGGTCCTAATGCCTGAAGCTCAGGTGGAGAAGAAATTGTGCAGGTGGCT
GAGGAAGAAATAGCAGGGAGT
Found at i:54974 original size:17 final size:17
Alignment explanation
Indices: 54952--54988 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
54942 AGAGGAAGGA
* *
54952 AGGGGAGGGGGAGGGGG
1 AGGGGAGGAGAAGGGGG
54969 AGGGGAGGAGAAGGGGG
1 AGGGGAGGAGAAGGGGG
54986 AGG
1 AGG
54989 AGAAGGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (17 bp):
AGGGGAGGAGAAGGGGG
Found at i:54989 original size:12 final size:12
Alignment explanation
Indices: 54957--54994 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54947 AAGGAAGGGG
* *
54957 AGGGGGAGGGGG
1 AGGGGGAGGAGA
54969 A-GGGGAGGAGA
1 AGGGGGAGGAGA
54980 AGGGGGAGGAGA
1 AGGGGGAGGAGA
54992 AGG
1 AGG
54995 AAGACATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.29, C:0.00, G:0.71, T:0.00
Consensus pattern (12 bp):
AGGGGGAGGAGA
Found at i:80493 original size:128 final size:129
Alignment explanation
Indices: 80264--80520 Score: 498
Period size: 128 Copynumber: 2.0 Consensus size: 129
80254 AACTTTAGGA
80264 AACAAAACGAGTCCATGTGAAACCAATTCAGAGAAATGTTAGGGAAGAAGAAACCAACCAAAATA
1 AACAAAACGAGTCCATGTGAAACCAATTCAGAGAAATGTTAGGGAAGAAGAAACCAACCAAAATA
80329 GAAATGAAGACGAAAGGAAAATAGAACTGAAATTTCAATAGTTTACCCATGAATCAACCATTAT
66 GAAATGAAGACGAAAGGAAAATAGAACTGAAATTTCAATAGTTTACCCATGAATCAACCATTAT
80393 AACAAAACGAGTCCATGTGAAACCAATTCAGAGAAATGTTA-GGAAGAAGAAACCAACCAAAATA
1 AACAAAACGAGTCCATGTGAAACCAATTCAGAGAAATGTTAGGGAAGAAGAAACCAACCAAAATA
*
80457 GAAATGAAGACGAAAGGAAAATAGAACTGGAATTTCAATAGTTTACCCATGAATCAACCATTAT
66 GAAATGAAGACGAAAGGAAAATAGAACTGAAATTTCAATAGTTTACCCATGAATCAACCATTAT
80521 TGCGGATACA
Statistics
Matches: 127, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
128 86 0.68
129 41 0.32
ACGTcount: A:0.49, C:0.16, G:0.17, T:0.19
Consensus pattern (129 bp):
AACAAAACGAGTCCATGTGAAACCAATTCAGAGAAATGTTAGGGAAGAAGAAACCAACCAAAATA
GAAATGAAGACGAAAGGAAAATAGAACTGAAATTTCAATAGTTTACCCATGAATCAACCATTAT
Found at i:83004 original size:56 final size:56
Alignment explanation
Indices: 82936--83054 Score: 202
Period size: 56 Copynumber: 2.1 Consensus size: 56
82926 GTACCCTAAA
* *
82936 CCCTCAAGTTAATGAAGGTTCAGGTTCTCAATGGCAACTATATATCTGAGTTCAAT
1 CCCTCAAGTTAATGAAGGTTCAGGTTCTCAATGACAACTACATATCTGAGTTCAAT
* *
82992 CTCTCAAGTTAATGAAGGTTCAGGTTCTCGATGACAACTACATATCTGAGTTCAAT
1 CCCTCAAGTTAATGAAGGTTCAGGTTCTCAATGACAACTACATATCTGAGTTCAAT
83048 CCCTCAA
1 CCCTCAA
83055 CCCGAAGTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (56 bp):
CCCTCAAGTTAATGAAGGTTCAGGTTCTCAATGACAACTACATATCTGAGTTCAAT
Found at i:86428 original size:47 final size:47
Alignment explanation
Indices: 86359--86448 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
86349 CCTGTGCTGT
86359 CACAGGATCATAAATGGGGGTGAAAACTATCCAACGGCTGCTTACAG
1 CACAGGATCATAAATGGGGGTGAAAACTATCCAACGGCTGCTTACAG
* *
86406 CACAGGGTCATAAATGGGGGTGAAAACTATCCAGCGGCTGCTT
1 CACAGGATCATAAATGGGGGTGAAAACTATCCAACGGCTGCTT
86449 GAAAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (47 bp):
CACAGGATCATAAATGGGGGTGAAAACTATCCAACGGCTGCTTACAG
Done.