Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018072.1 Corchorus olitorius cultivar O-4 contig18105, 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: 45289
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2308 original size:29 final size:30
Alignment explanation
Indices: 2248--2326 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
2238 CTAAATACCA
**
2248 AAAAAAATCCCTTATGTTTTGCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTT-CTTTCAGGAC
*
2279 AAAACAATCCCTTATGTTTT-TTTCAGGAC
1 AAAAAAATCCCTTATGTTTTCTTTCAGGAC
** *
2308 AAATTAATCCCTTACGTTT
1 AAAAAAATCCCTTATGTTT
2327 CAAAAATGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.55
31 19 0.45
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (30 bp):
AAAAAAATCCCTTATGTTTTCTTTCAGGAC
Found at i:2514 original size:30 final size:30
Alignment explanation
Indices: 2450--2544 Score: 145
Period size: 31 Copynumber: 3.1 Consensus size: 30
2440 AAGGGACTGA
2450 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAATATAAGGGA-TTT
* *
2481 TTTGTTCCAAAAGAAAAACATAAGGGATTT
1 TTTGTCCCAAAAGAAAAATATAAGGGATTT
*
2511 TTTGTCCCAAAAGAAAAATATAAGAGAATTT
1 TTTGTCCCAAAAGAAAAATATAAG-GGATTT
2542 TTT
1 TTT
2545 AGTATTTAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 25 0.43
31 33 0.57
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAAATATAAGGGATTT
Found at i:3342 original size:125 final size:125
Alignment explanation
Indices: 3157--3394 Score: 327
Period size: 126 Copynumber: 1.9 Consensus size: 125
3147 CTTATTTTTC
* * * **
3157 AAATATATTTTTTAAATGCCATTTTTATACTTTTACAATTTTACTCAATTAAAAACTCTA-TTTT
1 AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
*
3221 ATTTAATCAAA-TCTAATATATTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
66 ATTTAATCAAATTC-AATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * ** *
3281 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAGTTTTATTTTACCAAAAATTCTATTTT
1 AAATATATTTCTTAAATGACATT-TTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTT
* *
3346 TATTTAATTAAATTCAATATTTTTATAACTATTTTATCTTTACCATTTT
65 TATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTT
3395 TTTAGGGAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
124 21 0.21
125 29 0.30
126 46 0.47
127 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.01, T:0.53
Consensus pattern (125 bp):
AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
ATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:3797 original size:29 final size:30
Alignment explanation
Indices: 3755--3828 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
3745 CTCATTTTTG
* *
3755 AAACGTAAGGGATTAATTTGTCCCCAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
* *
3784 AAACATAAGGGATTATTTTGTCCTAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
3815 AAACATAAGGGATT
1 AAACATAAGGGATT
3829 TTTCTGGGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.26
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:4493 original size:192 final size:195
Alignment explanation
Indices: 4045--4540 Score: 719
Period size: 192 Copynumber: 2.5 Consensus size: 195
4035 GGACAATCAA
* * *
4045 TTATCTCAGCAGATTCCAAGTGTGGAAGTCCTAGAGCCACAGTGATTGGGAACACATATTTCATG
1 TTATCTTAGCAGATTCCAAGTGTGGAAGTCCTTGAGCCAAAGTGATTGGGAACACATATTTCATG
* * * *
4110 CTTTTGCAACCAATAATCCTAAGTATTTTCAATTTAGGCCAGCACAAAGGAAGACTTTGCAGCAC
66 CTTTTGCAACCACTAATCTTAAGTGTTTTCAATTTAGGCCAGCACAAAGGAAGACCTTGCAGCAC
* **
4175 GTTTGAAACTATGGTTTCATCCCCATTTTGTTCTTCCATGATCAAGTATTCCAAAGACTTGCACT
131 GTTTGAAACTACGGTTT-AT--CCATTTTGTTCTTCCATGATCAAGTATTCCAAAGACTCACACT
4240 CCT
193 CCT
**
4243 TTATCTTAGCAGATTCCAAGTGTGGAAGTCCTTGAGCCAAAGTGATTGTAAACACATATTTCATG
1 TTATCTTAGCAGATTCCAAGTGTGGAAGTCCTTGAGCCAAAGTGATTGGGAACACATATTTCATG
* * *
4308 CTTTTGCAACCACTTATCTTAAATGTTTTCAATTTAGGCCAGCACAAAGGAAGACCTTGCTGCAC
66 CTTTTGCAACCACTAATCTTAAGTGTTTTCAATTTAGGCCAGCACAAAGGAAGACCTTGCAGCAC
* * *
4373 GTTTGAAACTACGG-TT-T-CATTTTGTTCTTCCATGATTAAGTATTCCAAAGACTCACAGTCTT
131 GTTTGAAACTACGGTTTATCCATTTTGTTCTTCCATGATCAAGTATTCCAAAGACTCACACTCCT
* * * *
4435 TTATCTTAGCAGATCCCAAGTGTGGAAGTCCTTGAGCCAGAGTGATTGGGAGCACATATTTCAAG
1 TTATCTTAGCAGATTCCAAGTGTGGAAGTCCTTGAGCCAAAGTGATTGGGAACACATATTTCATG
* * *
4500 CTCTTGCAACTACTAATCTCAAGTGTTTTCAATTTAGGCCA
66 CTTTTGCAACCACTAATCTTAAGTGTTTTCAATTTAGGCCA
4541 CAACATGTTC
Statistics
Matches: 269, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
192 135 0.50
195 1 0.00
197 2 0.01
198 131 0.49
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (195 bp):
TTATCTTAGCAGATTCCAAGTGTGGAAGTCCTTGAGCCAAAGTGATTGGGAACACATATTTCATG
CTTTTGCAACCACTAATCTTAAGTGTTTTCAATTTAGGCCAGCACAAAGGAAGACCTTGCAGCAC
GTTTGAAACTACGGTTTATCCATTTTGTTCTTCCATGATCAAGTATTCCAAAGACTCACACTCCT
Found at i:6049 original size:22 final size:22
Alignment explanation
Indices: 6022--6097 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
6012 TAACCCTATC
*
6022 TTTTACTTTTCATCATCCTTGT
1 TTTTACTTTTCATCAACCTTGT
* *
6044 TTTTACAAGTTGTGATCAACCTTGT
1 TTTTAC---TTTTCATCAACCTTGT
* *
6069 CATTTACTTTTCATCACCCTTGT
1 -TTTTACTTTTCATCAACCTTGT
6092 TTTTAC
1 TTTTAC
6098 AAGGTGTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 11 0.26
23 13 0.31
25 13 0.31
26 5 0.12
ACGTcount: A:0.18, C:0.22, G:0.08, T:0.51
Consensus pattern (22 bp):
TTTTACTTTTCATCAACCTTGT
Found at i:7813 original size:5 final size:5
Alignment explanation
Indices: 7796--7835 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
7786 GTTTTCGTTT
7796 TTTTG TTTT- TTTTG TTTTTG TTTTG TTTTCG TTTTG TTTT
1 TTTTG TTTTG TTTTG -TTTTG TTTTG TTTT-G TTTTG TTTT
7836 TGTTACGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.12
5 18 0.56
6 10 0.31
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:7819 original size:11 final size:11
Alignment explanation
Indices: 7796--7839 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
7786 GTTTTCGTTT
7796 TTTTG-TTTT-
1 TTTTGTTTTTG
7805 TTTTGTTTTTG
1 TTTTGTTTTTG
*
7816 TTTTGTTTTCG
1 TTTTGTTTTTG
7827 TTTTGTTTTTG
1 TTTTGTTTTTG
7838 TT
1 TT
7840 ACGCTGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 5 0.16
10 4 0.13
11 22 0.71
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:7836 original size:6 final size:6
Alignment explanation
Indices: 7786--7839 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
7776 GTTTGGTATC
* *
7786 GTTTTC GTTTTT -TTGTTT -TTTTT GTTTTT G-TTTT GTTTTC G-TTTT
1 GTTTTT GTTTTT GTT-TTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
7831 GTTTTT GTT
1 GTTTTT GTT
7840 ACGCTGTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 14 0.34
6 27 0.66
ACGTcount: A:0.00, C:0.04, G:0.17, T:0.80
Consensus pattern (6 bp):
GTTTTT
Found at i:10599 original size:2 final size:2
Alignment explanation
Indices: 10592--10623 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10582 ATTAATACAT
10592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10624 CTGATTTTCT
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):
TA
Found at i:14022 original size:1 final size:1
Alignment explanation
Indices: 14016--14044 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
14006 CTCAGCCTGC
14016 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14045 CAATTATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16226 original size:22 final size:21
Alignment explanation
Indices: 16192--16423 Score: 110
Period size: 22 Copynumber: 10.5 Consensus size: 21
16182 GTCTCTATGC
16192 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAAGA
* * *
16213 TGGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AAGA
* *
16236 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATA-AGA
*
16258 GGTT-TCCAAAATTTCATAGGGA
1 GGTTAT-CAAAATTTCATA-AGA
* **
16280 AGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAAG-A
*
16302 AGTTATCAAAATTTCAT-AGTA
1 GGTTATCAAAATTTCATAAG-A
*
16323 TGGTTA-CAAAAATTTCATAGGATCA
1 -GGTTATC-AAAATTTCATA--A-GA
* * **
16348 AGTTATTAAAATTTTTTAAGAA
1 GGTTATCAAAATTTCATAAG-A
** * *
16370 GGTTATTGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATA-AGA
* * *
16392 GGTTATCACAATTTTATAAAAA
1 GGTTATCAAAATTTCAT-AAGA
16414 GGTTATCAAA
1 GGTTATCAAA
16424 GAGATTATCA
Statistics
Matches: 161, Mismatches: 34, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
21 7 0.04
22 133 0.83
23 6 0.04
24 13 0.08
25 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAAGA
Found at i:16307 original size:66 final size:67
Alignment explanation
Indices: 16223--16553 Score: 230
Period size: 66 Copynumber: 4.8 Consensus size: 67
16213 TGGTTATTAT
* * *
16223 AATTTCATGAGG-AGGTTATCAAAATTTCATAGTGTGGTTTCCAAAATTTCATAGG-GAAGTTAT
1 AATTTCATG-GGAAGGTTATCAAAATTTCATAGTGTGGTTACAAAAATTTCATAGGACAAGTTAT
16286 CAA
65 CAA
* *
16289 AATTTCATGGGAAAGTTATCAAAATTTCATAGTATGGTTACAAAAATTTCATAGGATCAAGTTAT
1 AATTTCATGGGAAGGTTATCAAAATTTCATAGTGTGGTTACAAAAATTTCATAGGA-CAAGTTAT
*
16354 TAA
65 CAA
** ** ** * *
16357 AATTTTTTAAGAAGGTTATTGAAATTTCATAGTGTGGTTATC-ACAATTTTATAAAAAGGTTATC
1 AATTTCATGGGAAGGTTATCAAAATTTCATAGTGTGGTTA-CAAAAATTTCAT----AGG--A-C
16421 AAAGAGATTATCAA
58 --A-AG-TTATCAA
* * ** * * *
16435 AATGTCATAGCGAGGTTAT-AAGAATTCCATAGTGTGGTTA-ACAAAATTTCATAAGA-AGGTTA
1 AATTTCATGGGAAGGTTATCAA-AATTTCATAGTGTGGTTACA-AAAATTTCATAGGACAAGTTA
16497 -CTAA
64 TC-AA
*
16501 TATTTCATAGGG-AGGTTATCAAAATTTCATAGTGTGGTTATC-AAAATTTCATA
1 AATTTCAT-GGGAAGGTTATCAAAATTTCATAGTGTGGTTA-CAAAAATTTCATA
16554 TGAAGGTTAT
Statistics
Matches: 209, Mismatches: 34, Indels: 44
0.73 0.12 0.15
Matches are distributed among these distances:
65 3 0.01
66 94 0.45
67 4 0.02
68 50 0.24
69 1 0.00
72 4 0.02
74 5 0.02
76 1 0.00
77 3 0.01
78 44 0.21
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (67 bp):
AATTTCATGGGAAGGTTATCAAAATTTCATAGTGTGGTTACAAAAATTTCATAGGACAAGTTATC
AA
Found at i:16312 original size:44 final size:45
Alignment explanation
Indices: 16193--16320 Score: 138
Period size: 44 Copynumber: 2.9 Consensus size: 45
16183 TCTCTATGCG
* * * *
16193 GTTATCAAAATTTCATAAGATGGTTATTATAATTTCAT-GAGGAG
1 GTTATCAAAATTTCATGAGATGGTTATCAAAATTTCATAGAGGAA
*
16237 GTTATCAAAATTTCAT-AGTGTGGTT-TCCAAAATTTCATAG-GGAA
1 GTTATCAAAATTTCATGAG-ATGGTTAT-CAAAATTTCATAGAGGAA
* **
16281 GTTATCAAAATTTCATGGGAAAGTTATCAAAATTTCATAG
1 GTTATCAAAATTTCATGAGATGGTTATCAAAATTTCATAG
16321 TATGGTTACA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
43 3 0.04
44 65 0.92
45 3 0.04
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (45 bp):
GTTATCAAAATTTCATGAGATGGTTATCAAAATTTCATAGAGGAA
Found at i:16540 original size:44 final size:42
Alignment explanation
Indices: 16428--17347 Score: 203
Period size: 44 Copynumber: 21.3 Consensus size: 42
16418 ATCAAAGAGA
* * * *
16428 TTATCAAAATGTCATAGCGAGGTTATAAGAATTCCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTATAA-AATTTCATAGGGAGG
* * *
16472 TTAACAAAATTTCATAAGAAGGTTACTAATATTTCATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTA-TAAAATTTCATAGGGAGG
* * *
16516 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAG-GAGGTTAT-AAAATTTCATAGGGAGG
* * * *
16560 TTATAAAAGTCTTAATTTCATAAGGA-G-TACCAAAATTTGATA-GAAGG
1 TTAT-CAA-----AATTTCAT-AGGAGGTTA-TAAAATTTCATAGGGAGG
* * ** *
16607 TTATC-AAATCTCATA-GAGTGATTATCGAAATTTCATAAAGATCGAA
1 TTATCAAAATTTCATAGGAG-G-TTAT-AAAATTTCATAGGGA--G-G
* * ** **
16653 TTATCAAAATTT-ATAGGAAGATTATCAAAATTTTATACTGTTG
1 TTATCAAAATTTCATAGG-AGGTTAT-AAAATTTCATAGGGAGG
* * ** **
16696 TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGAAA
1 TTATCAAAATTTCATAG-GAGGTTAT-AAAATTTCATAGGGAGG
* * * * * *
16740 ATATCAAAATTTCATA-GAGGAGTCAACAAAATTTTATAGAGAAG
1 TTATCAAAATTTCATAGGA-G-GT-TATAAAATTTCATAGGGAGG
* * * ** * *
16784 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCAT-AGGAGGTTAT-AAAATTTCATAGGGAGG
* * * *
16828 TTACCAAAATTTCATA-GTGG---T---ATTTC-TGGGGAAG
1 TTATCAAAATTTCATAGGAGGTTATAAAATTTCATAGGGAGG
* ** *
16862 TTATCAAAATTTCATAGTATGGTTACCAAA--T--TAGGAAGG
1 TTATCAAAATTTCATAGGA-GGTTATAAAATTTCATAGGGAGG
* * * * *
16901 TTATTAAACTTTTACTATGGA-GTAATCAAAACTTC--AGGGAGG
1 TTATCAAAATTTCA-TA-GGAGGTTAT-AAAATTTCATAGGGAGG
* * **
16943 ATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATA-GGAGGTTAT-AAAATTTCATAG-GGAGG
* * *
16987 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGGA-GGTTAT-AAAATTTCATAGGGAGG
* * **
17031 TTAACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTAT-AAAATTTCATAGGGAGG
* * * * *
17075 TTATCAAAA-TT--T-GTA-GTCATCAAGATTTCATAAGAAGG
1 TTATCAAAATTTCATAGGAGGTTAT-AAAATTTCATAGGGAGG
* * * *
17113 TTATTAAAATTTTATAGGGAGGTTTATTAAAATTTTATAGCGAGG
1 TTATCAAAATTTCATA-GGAGG-TTA-TAAAATTTCATAGGGAGG
* * * * * * *
17158 TTATCACAATTTCATAGTGTGATTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGGTTAT-AAAATTTCATAGGGAGG
* * * ** * *
17202 TTA-CTAACAA-TTCATATGGAGGTTTTTCAATTTTCATAACGTGA
1 TTATC-AA-AATTTCATA-GGAGG-TTATAAAATTTCATAGGGAGG
* * * **
17246 TTATCAATATATCATATGGAGGTTATCAACATCTT-ATAGTGTTGG
1 TTATCAAAATTTCATA-GGAGGTTAT-AAAAT-TTCATAG-GGAGG
* * *
17291 TTATCAAAATTTCATAGTGAGGTCT-TCAAAATTCCTTAAGGAGG
1 TTATCAAAATTTCATAG-GAGGT-TAT-AAAATTTCATAGGGAGG
*
17335 TTAACAAAATTTC
1 TTATCAAAATTTC
17348 TTAAGAAGGT
Statistics
Matches: 637, Mismatches: 164, Indels: 150
0.67 0.17 0.16
Matches are distributed among these distances:
34 16 0.03
35 4 0.01
36 2 0.00
38 27 0.04
39 24 0.04
40 14 0.02
41 9 0.01
42 46 0.07
43 31 0.05
44 312 0.49
45 84 0.13
46 27 0.04
47 15 0.02
48 14 0.02
49 1 0.00
50 9 0.01
51 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (42 bp):
TTATCAAAATTTCATAGGAGGTTATAAAATTTCATAGGGAGG
Found at i:16563 original size:22 final size:21
Alignment explanation
Indices: 16428--16844 Score: 154
Period size: 22 Copynumber: 18.8 Consensus size: 21
16418 ATCAAAGAGA
* *
16428 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-AAGG
* **
16450 TTAT-AAGAATTCCATAGTGTGG
1 TTATCAA-AATTTCATAG-AAGG
*
16472 TTAACAAAATTTCATAAGAAGG
1 TTATCAAAATTTCAT-AGAAGG
* *
16494 TTA-CTAATATTTCATAGGGAGG
1 TTATC-AAAATTTCATA-GAAGG
**
16516 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-AAGG
16538 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GAAGG
* *
16560 TTAT-AAAAGTCTTAATTTCATAAGG
1 TTATCAAAA-T-TTCA--T-AGAAGG
* * *
16585 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGAAGG
*
16607 TTATC-AAATCTCATAG-AGTG
1 TTATCAAAATTTCATAGAAG-G
*
16627 ATTATCGAAATTTCATA-AAGATCG
1 -TTATCAAAATTTCATAGAAG---G
*
16651 AATTATCAAAATTT-ATAGGAAGA
1 --TTATCAAAATTTCATA-GAAGG
* **
16674 TTATCAAAATTTTATACTG-TTG
1 TTATCAAAATTTCATA--GAAGG
* *
16696 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-AAGG
* *
16718 TTATCAAAATTACATAATGAA-A
1 TTATCAAAATTTCAT-A-GAAGG
* *
16740 ATATCAAAATTTCATAGAGGAG
1 TTATCAAAATTTCATAGAAG-G
* * * *
16762 TCAACAAAATTTTATAGAGAAG
1 TTATCAAAATTTCATAGA-AGG
*
16784 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
16806 TTATCAAATTTTCA-A-AATGTG
1 TTATCAAAATTTCATAGAA-G-G
*
16827 ATTACCAAAATTTCATAG
1 -TTATCAAAATTTCATAG
16845 TGGTATTTCT
Statistics
Matches: 299, Mismatches: 58, Indels: 74
0.69 0.13 0.17
Matches are distributed among these distances:
19 3 0.01
20 15 0.05
21 32 0.11
22 199 0.67
23 14 0.05
24 5 0.02
25 20 0.07
26 7 0.02
27 4 0.01
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGAAGG
Found at i:16971 original size:22 final size:22
Alignment explanation
Indices: 16938--17347 Score: 185
Period size: 22 Copynumber: 18.8 Consensus size: 22
16928 AAAACTTCAG
*
16938 GGAGGATATCAAAATTTCATAT
1 GGAGGTTATCAAAATTTCATAT
*
16960 GAAGGTTATCAAAATTTCATAGT
1 GGAGGTTATCAAAATTTCATA-T
** *
16983 TTA-GTTTTCAAAATTTCATA-
1 GGAGGTTATCAAAATTTCATAT
* *
17003 AGAGGGTTATCAAAATTTCATAG
1 GGA-GGTTATCAAAATTTCATAT
* *
17026 GGAGATTAACAAAATTTCATAAT
1 GGAGGTTATCAAAATTTCAT-AT
** *
17049 -GAGGTTATCAAAAAATCATAG
1 GGAGGTTATCAAAATTTCATAT
17070 GGAGGTTATCAAAA--T--T-T
1 GGAGGTTATCAAAATTTCATAT
* * * *
17087 GTA-GTCATCAAGATTTCATAA
1 GGAGGTTATCAAAATTTCATAT
* * * *
17108 GAAGGTTATTAAAATTTTATAG
1 GGAGGTTATCAAAATTTCATAT
* *
17130 GGAGGTTTATTAAAATTTTATA-
1 GGAGG-TTATCAAAATTTCATAT
*
17152 GCGAGGTTATCACAATTTCATAGT
1 G-GAGGTTATCAAAATTTCATA-T
*
17176 GTGA--TTATCAAAATTTCAGAGT
1 G-GAGGTTATCAAAATTTCATA-T
17198 GTGA--TTA-CTAACAA-TTCATAT
1 G-GAGGTTATC-AA-AATTTCATAT
* * *
17219 GGAGGTTTTTC-AATTTTCATAA
1 GGAGG-TTATCAAAATTTCATAT
* * * * *
17241 CGTGATTATCAATATATCATAT
1 GGAGGTTATCAAAATTTCATAT
*
17263 GGAGGTTATCAACATCTT-ATAGT
1 GGAGGTTATCAAAAT-TTCATA-T
**
17286 GTTGGTTATCAAAATTTCATA-
1 GGAGGTTATCAAAATTTCATAT
* * *
17307 GTGAGGTCT-TCAAAATTCCTTAA
1 G-GAGGT-TATCAAAATTTCATAT
*
17330 GGAGGTTAACAAAATTTC
1 GGAGGTTATCAAAATTTC
17348 TTAAGAAGGT
Statistics
Matches: 296, Mismatches: 61, Indels: 62
0.71 0.15 0.15
Matches are distributed among these distances:
16 8 0.03
17 2 0.01
18 2 0.01
20 5 0.02
21 13 0.04
22 214 0.72
23 48 0.16
24 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
GGAGGTTATCAAAATTTCATAT
Found at i:17143 original size:23 final size:23
Alignment explanation
Indices: 17113--17159 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
17103 CATAAGAAGG
*
17113 TTATTAAAATTTTATAGGGAGGT
1 TTATTAAAATTTTATAGCGAGGT
17136 TTATTAAAATTTTATAGCGAGGT
1 TTATTAAAATTTTATAGCGAGGT
17159 T
1 T
17160 ATCACAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (23 bp):
TTATTAAAATTTTATAGCGAGGT
Found at i:17188 original size:105 final size:104
Alignment explanation
Indices: 16990--17191 Score: 251
Period size: 105 Copynumber: 1.9 Consensus size: 104
16980 AGTTTAGTTT
* *
16990 TCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 TCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAACGAGGTT
*
17055 ATCAAAAAATCATAGGGAGGTTATCAAAATTTGTAGTCA
66 ATCAAAAAATCATAGGGAGATTATCAAAATTTGTAGTCA
* * * * ** * *
17094 TCAAGATTTCATAAGAAGGTTATTAAAATTTTATAGGGAGGTTTATTAAAATTTTATAGCGAGGT
1 TCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGGGA-GATTAACAAAATTTCATAACGAGGT
* ** * *
17159 TATCACAATTTCATAGTGTGATTATCAAAATTT
65 TATCAAAAAATCATAGGGAGATTATCAAAATTT
17192 CAGAGTGTGA
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
104 35 0.43
105 46 0.57
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (104 bp):
TCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAACGAGGTT
ATCAAAAAATCATAGGGAGATTATCAAAATTTGTAGTCA
Found at i:17350 original size:22 final size:22
Alignment explanation
Indices: 17317--17368 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
17307 GTGAGGTCTT
* *
17317 CAAAATTCCTTAAGGAGGTTAA
1 CAAAATTTCTTAAGAAGGTTAA
17339 CAAAATTTCTTAAGAAGGTTAA
1 CAAAATTTCTTAAGAAGGTTAA
*
17361 AAAAATTT
1 CAAAATTT
17369 ATATAAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (22 bp):
CAAAATTTCTTAAGAAGGTTAA
Found at i:17452 original size:22 final size:22
Alignment explanation
Indices: 17400--17452 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
17390 GATAGTATCA
* *
17400 TTATTAAAGTTTTATAAGAAGG
1 TTATAAAAATTTTATAAGAAGG
* *
17422 TTATTAAAATTTTATAAGGA-G
1 TTATAAAAATTTTATAAGAAGG
17443 TTCATAAAAA
1 TT-ATAAAAA
17453 ATAGTGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATAAAAATTTTATAAGAAGG
Found at i:17585 original size:132 final size:132
Alignment explanation
Indices: 17429--17669 Score: 473
Period size: 132 Copynumber: 1.8 Consensus size: 132
17419 AGGTTATTAA
17429 AATTTTATAAGGAGTTCATAAAAAATAGTGTAATTATCATAATTTAATAGGGAGGATATCATAAT
1 AATTTTATAAGGAGTTCATAAAAAATAGTGTAATTATCATAATTTAATAGGGAGGATATCATAAT
17494 TTCATATATGAATATTTCATTTAAACACATTGGGTCACATGCAATTCACGTTAGAACTCCTTATA
66 TTCATATATGAATATTTCATTTAAACACATTGGGTCACATGCAATTCACGTTAGAACTCCTTATA
17559 TG
131 TG
17561 AATTTTATAAGGAGTTCATAAAAAATAGTGTAATTATCATAATTTAATAGGGAGGATATCATAAT
1 AATTTTATAAGGAGTTCATAAAAAATAGTGTAATTATCATAATTTAATAGGGAGGATATCATAAT
*
17626 TTCATATATGAATATTTCATTTAAACACATTGGGTCACGTGCAA
66 TTCATATATGAATATTTCATTTAAACACATTGGGTCACATGCAA
17670 CGCACGTGAA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 108 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (132 bp):
AATTTTATAAGGAGTTCATAAAAAATAGTGTAATTATCATAATTTAATAGGGAGGATATCATAAT
TTCATATATGAATATTTCATTTAAACACATTGGGTCACATGCAATTCACGTTAGAACTCCTTATA
TG
Found at i:19819 original size:92 final size:93
Alignment explanation
Indices: 19633--19849 Score: 230
Period size: 92 Copynumber: 2.4 Consensus size: 93
19623 AACAACAGTT
* * * * * **
19633 GCATTCCGATTATACATCAAGGTATAATGGTG-CATCAAAGTAAAAGATGGTTATGTGAATTTTT
1 GCATTCCTACTATACATAAAGGTATAATGGTGCCATCAAAGTAAAAGATGGTAATGAGAATTCCT
19697 ATTATATGCAGTAAACGGCACAAGAATG
66 ATTATATGCAGTAAACGGCACAAGAATG
* * * *
19725 GCATTCCTA-TATACATTAAGGTATAATGGTGCCATCCAAA-TTAAGGTTGGTAATGAGAATTCC
1 GCATTCCTACTATACATAAAGGTATAATGGTGCCAT-CAAAGTAAAAGATGGTAATGAGAATTCC
**
19788 TA-T-TATGCAGTTAAA-GGCACAATGTGGTG
65 TATTATATGCAG-TAAACGGCACAA-G-AATG
*
19817 GCATTCCTACTATACATAAAGGTATAGTGGTGC
1 GCATTCCTACTATACATAAAGGTATAATGGTGC
19850 TAGTTAATAT
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
90 14 0.13
91 27 0.25
92 40 0.38
93 25 0.24
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (93 bp):
GCATTCCTACTATACATAAAGGTATAATGGTGCCATCAAAGTAAAAGATGGTAATGAGAATTCCT
ATTATATGCAGTAAACGGCACAAGAATG
Found at i:28802 original size:36 final size:36
Alignment explanation
Indices: 28755--28824 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
28745 TTCAATAACC
* *
28755 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
28791 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
28825 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:29727 original size:205 final size:200
Alignment explanation
Indices: 29345--29748 Score: 718
Period size: 201 Copynumber: 2.0 Consensus size: 200
29335 TTAATAACTT
* *
29345 TATCGATGATGAATGTTATTAATTTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAAGA
1 TATCAATGATGAATGTTATTAATTTTTTAAGTTTAAAATTACTAACAAAGTTGTAGTGAATAAGA
*
29410 TACAACACATTATTATTATATATAAAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTGATT
66 TACAACACATTACTATTATATATAAAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTGATT
29475 TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGA
131 TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCGA
29540 TTTATA
195 TTTATA
*
29546 TATCAATGGTGAATGTTATTAATTTTTTAAGTTTAAAATTACTAACAAAGTTGTAGTGAATAAGA
1 TATCAATGATGAATGTTATTAATTTTTTAAGTTTAAAATTACTAACAAAGTTGTAGTGAATAAGA
29611 TACAACACATTACTATTATATATATAGAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGTT
66 TACAACACATTACTATTATATATA-A-AACTATACC--AAAAAAATTAGTTGAACATTAGTGGTT
*
29676 GATTTATTAAATTAAATTAGATCAATGTCGAACAAAATTTCAAAATTATAAAAGATATTAAGATC
127 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
29741 CGATTTAT
192 CGATTTAT
29749 TTATTATTAA
Statistics
Matches: 194, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
201 85 0.44
202 1 0.01
203 9 0.05
204 14 0.07
205 85 0.44
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (200 bp):
TATCAATGATGAATGTTATTAATTTTTTAAGTTTAAAATTACTAACAAAGTTGTAGTGAATAAGA
TACAACACATTACTATTATATATAAAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTGATT
TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGAT
TTATA
Found at i:29858 original size:25 final size:24
Alignment explanation
Indices: 29824--29870 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
29814 ACGTTTGCAC
29824 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
29849 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
29871 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:29915 original size:39 final size:40
Alignment explanation
Indices: 29861--29941 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
29851 ATACCTAAGA
*
29861 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
29900 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
29940 AT
1 AT
29942 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:32362 original size:31 final size:30
Alignment explanation
Indices: 32290--32365 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
32280 TAAAACCAAA
32290 TTGTAAGTAGAGGGACCAAATTGACAGTTT
1 TTGTAAGTAGAGGGACCAAATTGACAGTTT
* * **
32320 TTAT-AGTAGAGGGATCAAATTGATCCTTTT
1 TTGTAAGTAGAGGGACCAAATTGA-CAGTTT
32350 TTGTAAGTAGAGGGAC
1 TTGTAAGTAGAGGGAC
32366 TTGTACGGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 18 0.47
30 10 0.26
31 10 0.26
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (30 bp):
TTGTAAGTAGAGGGACCAAATTGACAGTTT
Found at i:32978 original size:22 final size:23
Alignment explanation
Indices: 32944--32986 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
32934 GTTTGGCATT
32944 AGAACAATCTCTAAG-GATGTGG
1 AGAACAATCTCTAAGCGATGTGG
32966 AGAACAGAT-TCTAAGCGATGT
1 AGAACA-ATCTCTAAGCGATGT
32987 CCACATATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (23 bp):
AGAACAATCTCTAAGCGATGTGG
Done.