Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016201.1 Corchorus capsularis cultivar CVL-1 contig16222, 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: 51292
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:2034 original size:22 final size:21
Alignment explanation
Indices: 2001--2125 Score: 78
Period size: 22 Copynumber: 5.7 Consensus size: 21
1991 TGATTACCAA
2001 AACGAGATTACCAAAATTTCAT
1 AACGAGA-TACCAAAATTTCAT
*
2023 AACGATGATACCGAAATTTCAT
1 AACGA-GATACCAAAATTTCAT
* *
2045 AA-GATGGTTACGAAAATTTCA-
1 AACGA--GATACCAAAATTTCAT
*
2066 AA-GAGAGGTTCCCAAAATTTCAT
1 AACGAGA---TACCAAAATTTCAT
*
2089 -ACGGAGGTCACCAAAATTTCAT
1 AAC-GAGAT-ACCAAAATTTCAT
*
2111 AAGGAGATTACCAAA
1 AACGAGA-TACCAAA
2126 TTTTGATAGG
Statistics
Matches: 80, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
19 1 0.01
21 7 0.09
22 65 0.81
23 4 0.05
24 3 0.04
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (21 bp):
AACGAGATACCAAAATTTCAT
Found at i:2125 original size:44 final size:44
Alignment explanation
Indices: 2010--2236 Score: 125
Period size: 44 Copynumber: 5.2 Consensus size: 44
2000 AAACGAGATT
* * * *
2010 ACCAAAATTTCATAACGA-TGA-TACCGAAATTTCATAAGATGGTT
1 ACCAAAATTTCATAA-GAGAGATTACCAAAATTTCATAGGA-GGTA
* * * *
2054 ACGAAAATTTCA-AAGAGAGGTTCCCAAAATTTCATACGGAGGTC
1 ACCAAAATTTCATAAGAGAGATTACCAAAATTTCATA-GGAGGTA
* *
2098 ACCAAAATTTCATAAG-GAGATTACCAAATTTTGATAGG-GTGTA
1 ACCAAAATTTCATAAGAGAGATTACCAAAATTTCATAGGAG-GTA
* * * *
2141 ACC-AAATTTCAT-AGCA-AGATTACCAAACTTTTATATGATGGTT
1 ACCAAAATTTCATAAG-AGAGATTACCAAAATTTCATAGGA-GGTA
** * * *
2184 ACTGAAATTTCATAACTA-AG-TTA-CAGAAATTTCATAGGGGGTT
1 ACCAAAATTTCATAA-GAGAGATTACCA-AAATTTCATAGGAGGTA
*
2227 ACTAAAATTT
1 ACCAAAATTT
2237 TATAGTAAAG
Statistics
Matches: 146, Mismatches: 24, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
41 2 0.01
42 30 0.21
43 29 0.20
44 76 0.52
45 9 0.06
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (44 bp):
ACCAAAATTTCATAAGAGAGATTACCAAAATTTCATAGGAGGTA
Found at i:2565 original size:22 final size:23
Alignment explanation
Indices: 2539--2583 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
2529 AGTGAATTTG
2539 AGAACA-TCAAAA-CAAAAATAAA
1 AGAACACT-AAAATCAAAAATAAA
*
2561 AGAACACTAAAATTAAAAATAAA
1 AGAACACTAAAATCAAAAATAAA
2584 GCCGAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.71, C:0.11, G:0.04, T:0.13
Consensus pattern (23 bp):
AGAACACTAAAATCAAAAATAAA
Found at i:5198 original size:55 final size:56
Alignment explanation
Indices: 5127--5239 Score: 185
Period size: 55 Copynumber: 2.0 Consensus size: 56
5117 GCGCGCGCAC
5127 ACACACACACACATATTTACCGGA-AAAAAAACAAATAAAAATG-AAAAAATAAATT
1 ACACACACACACATATTTA-CGGACAAAAAAACAAATAAAAATGAAAAAAATAAATT
* *
5182 ACACACACACATATATTTACTGACAAAAAAACAAATAAAAATGAAAAAAATAAATT
1 ACACACACACACATATTTACGGACAAAAAAACAAATAAAAATGAAAAAAATAAATT
5238 AC
1 AC
5240 TCCATTGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
54 3 0.06
55 37 0.69
56 14 0.26
ACGTcount: A:0.62, C:0.16, G:0.04, T:0.18
Consensus pattern (56 bp):
ACACACACACACATATTTACGGACAAAAAAACAAATAAAAATGAAAAAAATAAATT
Found at i:6113 original size:3 final size:3
Alignment explanation
Indices: 6107--6148 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
6097 TATTATTATT
6107 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6149 CATATTTAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8049 original size:22 final size:21
Alignment explanation
Indices: 8021--8250 Score: 162
Period size: 22 Copynumber: 10.5 Consensus size: 21
8011 GGTCTATGTG
8021 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
8043 TGGTTATTATAATTTCAT-GA
1 TGGTTATCAAAATTTCATAGA
8063 -GGTTATCAAAATTTCATAG-
1 TGGTTATCAAAATTTCATAGA
*
8082 TGCAGTTACCAAAATTTCATATGGA
1 TG--GTTATCAAAATTTCATA--GA
*
8107 -AGTTATCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATA-GA
** * *
8128 AAGTTATCAAAAATTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
8150 TGGTTATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATA-GA
* *
8172 TCAGGTTATTAAAATTTCTTATGA
1 T--GGTTATCAAAATTTCATA-GA
* ** *
8196 AGGTTATTGAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
* *
8218 TGGTTATCACAATTTTATAGAA
1 TGGTTATCAAAATTTCATAG-A
*
8240 AGGTTATCAAA
1 TGGTTATCAAA
8251 GAGATTATAA
Statistics
Matches: 165, Mismatches: 30, Indels: 26
0.75 0.14 0.12
Matches are distributed among these distances:
19 15 0.09
20 4 0.02
21 4 0.02
22 122 0.74
23 1 0.01
24 19 0.12
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATAGA
Found at i:8213 original size:68 final size:66
Alignment explanation
Indices: 8018--8246 Score: 263
Period size: 68 Copynumber: 3.5 Consensus size: 66
8008 TCTGGTCTAT
* *
8018 GTGTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTC-ATG-AGGTTATCAAAATTTCAT
1 GTGTGGTTATCAAAATTTCATAGGATAGGTTATTAAAATTTCTATGAAGGTTATCAAAATTTCAT
8080 A
66 A
** * * * *
8081 GTGCAGTTACCAAAATTTCATATGGA-A-GTTATCAAAATTTCATATGAAAGTTATCAAAAATTC
1 GTGTGGTTATCAAAATTTCATA-GGATAGGTTATTAAAATTTC-TATGAAGGTTATCAAAATTTC
8144 ATA
64 ATA
**
8147 GTGTGGTTATCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTATGAAGGTTATTGAAATTTC
1 GTGTGGTTATCAAAATTTCATAGGAT-AGGTTATTAAAATTTC-TATGAAGGTTATCAAAATTTC
8212 ATA
64 ATA
* * *
8215 GTGTGGTTATCACAATTTTATA-GAAAGGTTAT
1 GTGTGGTTATCAAAATTTCATAGGATAGGTTAT
8247 CAAAGAGATT
Statistics
Matches: 138, Mismatches: 20, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
63 31 0.22
64 2 0.01
65 6 0.04
66 43 0.31
67 3 0.02
68 53 0.38
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (66 bp):
GTGTGGTTATCAAAATTTCATAGGATAGGTTATTAAAATTTCTATGAAGGTTATCAAAATTTCAT
A
Found at i:8354 original size:22 final size:21
Alignment explanation
Indices: 8315--8378 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
8305 AAATTCTATA
*
8315 AGGAGGTTA-CTAATATTTCACG
1 AGGAGGTTATC-AAAATTTCA-G
* *
8337 GGGAGGTTATCAAAATTTCAT
1 AGGAGGTTATCAAAATTTCAG
*
8358 AGTATGGTTATCAAAATTTCA
1 AGGA-GGTTATCAAAATTTCA
8379 TATGAAGGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.91
23 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (21 bp):
AGGAGGTTATCAAAATTTCAG
Found at i:8379 original size:22 final size:22
Alignment explanation
Indices: 8341--8626 Score: 106
Period size: 22 Copynumber: 12.8 Consensus size: 22
8331 TTCACGGGGA
8341 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
*
8363 GGTTATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGT-AT
* *
8385 GGTTAT-AAAAGTCTCAATTTCA-TAC
1 GGTTATCAAAA-TTTC-A--T-AGTAT
* * * *
8410 GGAGTACCAAAATTTGATAGAAT
1 GG-TTATCAAAATTTCATAGTAT
**
8433 -GTTATC-AAACCTCATAG-AGT
1 GGTTATCAAAATTTCATAGTA-T
* * * *
8453 GATTATCTAAATCTCATAGAGAT
1 GGTTATCAAAATTTCATAG-TAT
* *
8476 CGGATTATCAAAATTT-ATAGGAA
1 -GG-TTATCAAAATTTCATAGTAT
* *
8499 GATTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTAT
* * *
8521 TGTTATCAAAATTTCAAAGCGA-
1 GGTTATCAAAATTTCATAG-TAT
* * *
8543 GGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCATAGTAT
* * *
8565 GATTATCCAAATTTCATAG-AG
1 GGTTATCAAAATTTCATAGTAT
* * * *
8586 GAGTCAGCAAAATTTTATAG-AGA
1 G-GTTATCAAAATTTCATAGTA-T
8609 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
8627 AAGATGTTAT
Statistics
Matches: 193, Mismatches: 50, Indels: 42
0.68 0.18 0.15
Matches are distributed among these distances:
19 1 0.01
20 9 0.05
21 26 0.13
22 119 0.62
23 7 0.04
24 6 0.03
25 15 0.08
26 6 0.03
27 4 0.02
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:8388 original size:44 final size:44
Alignment explanation
Indices: 8340--9041 Score: 156
Period size: 44 Copynumber: 16.4 Consensus size: 44
8330 TTTCACGGGG
*
8340 AGGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGGA
* * * * *
8384 AGGTTAT-AAAAGTCTCAATTTCA-TACGGAGTACCAAAATTTGATA-GA
1 AGGTTATCAAAA-TTTC-A--T-AGTATGG-TTATCAAAATTTCATAGGA
* ** * * *
8431 ATGTTATC-AAACCTCATAG-AGTGATTATCTAAATCTCATAGAGA
1 AGGTTATCAAAATTTCATAGTA-TGGTTATCAAAATTTCATAG-GA
* * * *
8475 TCGGATTATCAAAATTT-ATAGGAAGATTATCAAAATTTCATAGTG-
1 -AGG-TTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAG-GA
** * * *
8520 TTGTTATCAAAATTTCAAAGCGA-GGTTATCAAAATTACATA--A
1 AGGTTATCAAAATTTCATAG-TATGGTTATCAAAATTTCATAGGA
* * * * * *
8562 TGTGATTATCCAAATTTCATAG-AGGAGTCAGCAAAATTTTATA-GA
1 AG-G-TTATCAAAATTTCATAGTATG-GTTATCAAAATTTCATAGGA
*
8607 GAGGTTATCAAAATTTCATAAAG-AT-GTTATCAAATTTTCA-A--A
1 -AGGTTATCAAAATTTCAT--AGTATGGTTATCAAAATTTCATAGGA
* * *
8649 ATGTGATTACCCAAATTTCATAG--TGG---T----ATTTC--AGGCG
1 A-G-G-TTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGG-A
* *
8686 AGGTTAACAAAATTTCATAGTATGGTTA-CCAAA--T--TAGGA
1 AGGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGGA
* ** * * * * *
8725 AGGTCATTGAACTTT--TATTATGGAGTAATTAAAATTTC--AGGG
1 AGGTTATCAAAATTTCATAGTAT-G-GTTATCAAAATTTCATAGGA
* ** *
8767 AGGATATCAAAATTTCATA-TGAAAGTTATCAAAATTTCATAAG-
1 AGGTTATCAAAATTTCATAGT-ATGGTTATCAAAATTTCATAGGA
* * * *
8810 AGAGTTATCAAACTTTCATAGTAT-GTAGATCAAAATTTTATAGGG
1 AG-GTTATCAAAATTTCATAGTATGGT-TATCAAAATTTCATAGGA
* * * * ** *
8855 AGATTAACAAAACTTCATAATGA-GGTTATCAAAAAATCATAGGG
1 AGGTTATCAAAATTTCATAGT-ATGGTTATCAAAATTTCATAGGA
8899 AGGTTATC-AAA-TT--T-GTAT--TTATCAAAATTTCATACGG-
1 AGGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCATA-GGA
* * *
8936 AGGTTATCAAAATTTTATAGGGA-GGTTTATCAAAATTTTATAGGA
1 AGGTTATCAAAATTTCATA-GTATGG-TTATCAAAATTTCATAGGA
* * * * *
8981 AGGTTTATCAAAATTTCATAGCGA-GATTATTACAATTTCATAGTA
1 AGG-TTATCAAAATTTCATAG-TATGGTTATCAAAATTTCATAGGA
* *
9026 TGATTATCAAAATTTC
1 AGGTTATCAAAATTTC
9042 GGAGTGTGAT
Statistics
Matches: 486, Mismatches: 98, Indels: 148
0.66 0.13 0.20
Matches are distributed among these distances:
34 16 0.03
35 5 0.01
36 4 0.01
37 28 0.06
38 7 0.01
39 17 0.03
40 8 0.02
41 3 0.01
42 49 0.10
43 32 0.07
44 182 0.37
45 48 0.10
46 52 0.11
47 21 0.04
48 14 0.03
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGGA
Found at i:8577 original size:66 final size:67
Alignment explanation
Indices: 8499--8643 Score: 170
Period size: 66 Copynumber: 2.2 Consensus size: 67
8489 TTTATAGGAA
* * ** * * * *
8499 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATG
1 GATTATCCAAATTTCATAGAGGAGTCAGCAAAATTTCAAAGAGAGGTTATCAAAATTACATAAAG
8564 -T
66 AT
* * *
8565 GATTATCCAAATTTCATAGAGGAGTCAGCAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAG
1 GATTATCCAAATTTCATAGAGGAGTCAGCAAAATTTCAAAGAGAGGTTATCAAAATTACATAAAG
8630 AT
66 AT
8632 G-TTAT-CAAATTT
1 GATTATCCAAATTT
8644 TCAAAATGTG
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
65 7 0.10
66 58 0.87
67 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (67 bp):
GATTATCCAAATTTCATAGAGGAGTCAGCAAAATTTCAAAGAGAGGTTATCAAAATTACATAAAG
AT
Found at i:8597 original size:88 final size:88
Alignment explanation
Indices: 8505--8671 Score: 228
Period size: 88 Copynumber: 1.9 Consensus size: 88
8495 GGAAGATTAT
* ** * *
8505 CAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAGAGAGGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
*
8569 ATCCAAATTTCATAGAGGAGTCAG
65 ACCCAAATTTCATAGAGGAGTCAG
* * * *
8593 CAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGATGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
8658 CCCAAATTTCATAG
66 CCCAAATTTCATAG
8672 TGGTATTTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
88 66 0.97
89 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (88 bp):
CAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCCAAATTTCATAGAGGAGTCAG
Found at i:8635 original size:22 final size:22
Alignment explanation
Indices: 8480--8646 Score: 112
Period size: 22 Copynumber: 7.6 Consensus size: 22
8470 AGAGATCGGA
8480 TTATCAAAATTT-ATAGGAAGA--
1 TTATCAAAATTTCATA--AAGATG
** *
8501 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGATG
* *
8523 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAA-AGATG
* *
8545 TTATCAAAATTACATAATG-TG
1 TTATCAAAATTTCATAAAGATG
* *
8566 ATTATCCAAATTTCATAGAGGA-G
1 -TTATCAAAATTTCATA-AAGATG
* * * * *
8589 TCAGCAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAAAGATG
8611 TTATCAAAATTTCATAAAGATG
1 TTATCAAAATTTCATAAAGATG
*
8633 TTATCAAATTTTCA
1 TTATCAAAATTTCA
8647 AAATGTGATT
Statistics
Matches: 112, Mismatches: 25, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 16 0.14
22 90 0.80
23 5 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGATG
Found at i:8646 original size:66 final size:65
Alignment explanation
Indices: 8480--8643 Score: 165
Period size: 66 Copynumber: 2.5 Consensus size: 65
8470 AGAGATCGGA
* ** * * *
8480 TTATCAAAATTT-ATAGGAAGA--TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCG
1 TTATCAAAATTTCATA--AAGATGTTATC-AAATTTCATAGAGGAGTCAGCAAAATTTCAAAGAG
8542 AGG
63 AGG
* * * *
8545 TTATCAAAATTACATAATG-TGATTATCCAAATTTCATAGAGGAGTCAGCAAAATTTTATAGAGA
1 TTATCAAAATTTCATAAAGATG-TTAT-CAAATTTCATAGAGGAGTCAGCAAAATTTCAAAGAGA
8609 GG
64 GG
8611 TTATCAAAATTTCATAAAGATGTTATCAAATTT
1 TTATCAAAATTTCATAAAGATGTTATCAAATTT
8644 TCAAAATGTG
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
64 2 0.02
65 18 0.22
66 58 0.72
67 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (65 bp):
TTATCAAAATTTCATAAAGATGTTATCAAATTTCATAGAGGAGTCAGCAAAATTTCAAAGAGAGG
Found at i:8799 original size:22 final size:22
Alignment explanation
Indices: 8755--9199 Score: 184
Period size: 22 Copynumber: 20.5 Consensus size: 22
8745 TGGAGTAATT
*
8755 AAAATTTC--AGGGAGGATATC
1 AAAATTTCATAGGGAGGTTATC
* * *
8775 AAAATTTCATATGAAAGTTATC
1 AAAATTTCATAGGGAGGTTATC
*
8797 AAAATTTCATA-AGAGAGTTATC
1 AAAATTTCATAGGGAG-GTTATC
* * * *
8819 AAACTTTCATA-GTATGTAGATC
1 AAAATTTCATAGGGAGGT-TATC
* * *
8841 AAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAGGGAGGTTATC
* **
8863 AAAACTTCATAATGAGGTTATC
1 AAAATTTCATAGGGAGGTTATC
**
8885 AAAAAATCATAGGGAGGTTATC
1 AAAATTTCATAGGGAGGTTATC
* *
8907 -AAA-TT--T--GTA-TTTATC
1 AAAATTTCATAGGGAGGTTATC
*
8922 AAAATTTCATACGGAGGTTATC
1 AAAATTTCATAGGGAGGTTATC
*
8944 AAAATTTTATAGGGAGGTTTATC
1 AAAATTTCATAGGGAGG-TTATC
* *
8967 AAAATTTTATAGGAAGGTTTATC
1 AAAATTTCATAGGGAGG-TTATC
* * *
8990 AAAATTTCATAGCGAGATTATT
1 AAAATTTCATAGGGAGGTTATC
* * *
9012 ACAATTTCATA-GTATGATTATC
1 AAAATTTCATAGGGA-GGTTATC
** * * *
9034 AAAATTTCGGAGTGTGATTA-C
1 AAAATTTCATAGGGAGGTTATC
* * * *
9055 TAACAA-TTCATATGGATGTTTTT
1 -AA-AATTTCATAGGGAGGTTATC
* ** * *
9078 AAATTTTCATAACGTGATTATC
1 AAAATTTCATAGGGAGGTTATC
* * *
9100 AATAAATT-ATATGGAGGTTCTC
1 AA-AATTTCATAGGGAGGTTATC
* * ***
9122 AACATCTCATAGTGTTTGTTATC
1 AAAATTTCATAG-GGAGGTTATC
* * *
9145 AAAATTTCATAGTGAGATTTTC
1 AAAATTTCATAGGGAGGTTATC
* *
9167 AAAATTTCTTAGAGAGGTTAAT-
1 AAAATTTCATAGGGAGGTT-ATC
9189 AAAATTTCATA
1 AAAATTTCATA
9200 AGATGGTTAA
Statistics
Matches: 305, Mismatches: 97, Indels: 44
0.68 0.22 0.10
Matches are distributed among these distances:
15 5 0.02
16 5 0.02
17 2 0.01
18 1 0.00
19 1 0.00
20 9 0.03
21 13 0.04
22 204 0.67
23 65 0.21
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGGGAGGTTATC
Found at i:9207 original size:22 final size:22
Alignment explanation
Indices: 9167--9227 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
9157 TGAGATTTTC
* *
9167 AAAATTTCTTAGAGAGGTT-AAT
1 AAAATTTCATA-AGAGGTTAAAA
9189 AAAATTTCATAAGATGGTTAAAA
1 AAAATTTCATAAGA-GGTTAAAA
*
9212 AAAATTT-ATAAAAGGT
1 AAAATTTCATAAGAGGT
9228 GTTCTCAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 6 0.18
22 19 0.56
23 9 0.26
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (22 bp):
AAAATTTCATAAGAGGTTAAAA
Found at i:21257 original size:24 final size:24
Alignment explanation
Indices: 21221--21269 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
21211 TAAAGTTATC
*
21221 TCCAAACTGCTGTATACTCAGTAT
1 TCCAAACTACTGTATACTCAGTAT
*
21245 TCCAAACTACTGTATACTTAGTAT
1 TCCAAACTACTGTATACTCAGTAT
21269 T
1 T
21270 TGGCTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (24 bp):
TCCAAACTACTGTATACTCAGTAT
Found at i:21969 original size:27 final size:30
Alignment explanation
Indices: 21909--21985 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 30
21899 ATATCCAAAA
* *
21909 AAAAAAATCCCTTATGTTTGTCTTTTGGGAC
1 AAAATAATCCCTTATGTTTGTCTTTT-GAAC
21940 AAAATAATCCCTTATGTTT-T-TTTT-AAC
1 AAAATAATCCCTTATGTTTGTCTTTTGAAC
* * *
21967 AAATTAATCTCTTACGTTT
1 AAAATAATCCCTTATGTTT
21986 AAAAAAATGC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 18 0.44
29 4 0.10
30 1 0.02
31 18 0.44
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (30 bp):
AAAATAATCCCTTATGTTTGTCTTTTGAAC
Found at i:22497 original size:44 final size:44
Alignment explanation
Indices: 22449--22571 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 44
22439 CATAGAAAAA
*
22449 TTATCAAAATTTCATAGTATGATTACCAAAATTTCATATAGAGG
1 TTATCAAAATTTCATAGTATGATTACCAAAATTTCATACAGAGG
* * *
22493 TTATCAAAACTTCATAGTAT-AGTTATCAAAATTTCATACAGATG
1 TTATCAAAATTTCATAGTATGA-TTACCAAAATTTCATACAGAGG
* ** * *
22537 TTACCAAAATTTCATAAAAAGGTTACCAAAATTTC
1 TTATCAAAATTTCATAGTATGATTACCAAAATTTC
22572 TTAGGGATGT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 1 0.02
44 65 0.98
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTATGATTACCAAAATTTCATACAGAGG
Found at i:22561 original size:22 final size:22
Alignment explanation
Indices: 22429--22571 Score: 101
Period size: 22 Copynumber: 6.5 Consensus size: 22
22419 TGACAATCAA
* *
22429 ACCAAAATTACATAGAAAA-ATT
1 ACCAAAATTTCATA-AAAAGGTT
* ** * *
22451 ATCAAAATTTCATAGTATGATT
1 ACCAAAATTTCATAAAAAGGTT
* *
22473 ACCAAAATTTCATATAGAGGTT
1 ACCAAAATTTCATAAAAAGGTT
* * * *
22495 ATCAAAACTTCATAGTATA-GTT
1 ACCAAAATTTCATA-AAAAGGTT
* * * *
22517 ATCAAAATTTCATACAGATGTT
1 ACCAAAATTTCATAAAAAGGTT
22539 ACCAAAATTTCATAAAAAGGTT
1 ACCAAAATTTCATAAAAAGGTT
22561 ACCAAAATTTC
1 ACCAAAATTTC
22572 TTAGGGATGT
Statistics
Matches: 97, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
21 3 0.03
22 91 0.94
23 3 0.03
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.32
Consensus pattern (22 bp):
ACCAAAATTTCATAAAAAGGTT
Found at i:22581 original size:44 final size:43
Alignment explanation
Indices: 22475--22622 Score: 127
Period size: 44 Copynumber: 3.4 Consensus size: 43
22465 GTATGATTAC
** * * * * * *
22475 CAAAATTTCATATAGAGGTTATCAAAACTTCATAGTATAGTTAT
1 CAAAATTTCATAGGGATGTTAACAAAATTTCAAAG-AAAGTTAA
** * *
22519 CAAAATTTCATACAGATGTTACCAAAATTTCATAA-AAAGGTTAC
1 CAAAATTTCATAGGGATGTTAACAAAATTTCA-AAGAAA-GTTAA
* *
22563 CAAAATTTCTTAGGGATGTTAATAAAATTTCAAATGAAAGTTAA
1 CAAAATTTCATAGGGATGTTAACAAAATTTCAAA-GAAAGTTAA
22607 CAAAATTTCATAGGGA
1 CAAAATTTCATAGGGA
22623 GAGAGGTTAC
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
43 4 0.05
44 78 0.91
45 4 0.05
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.32
Consensus pattern (43 bp):
CAAAATTTCATAGGGATGTTAACAAAATTTCAAAGAAAGTTAA
Found at i:22583 original size:22 final size:21
Alignment explanation
Indices: 22453--22618 Score: 113
Period size: 22 Copynumber: 7.6 Consensus size: 21
22443 GAAAAATTAT
22453 CAAAATTTCAT-AGTATGATTAC
1 CAAAATTTCATAAG-ATG-TTAC
* *
22475 CAAAATTTCATATAGAGGTTAT
1 CAAAATTTCATA-AGATGTTAC
* *
22497 CAAAACTTCAT-AGTATAGTTAT
1 CAAAATTTCATAAG-AT-GTTAC
22519 CAAAATTTCATACAGATGTTAC
1 CAAAATTTCATA-AGATGTTAC
* *
22541 CAAAATTTCATAAAAAGGTTAC
1 CAAAATTTCAT-AAGATGTTAC
* * *
22563 CAAAATTTCTTAGGGATGTTAA
1 CAAAATTTCATA-AGATGTTAC
* * *
22585 TAAAATTTCA-AATGAAAGTTAA
1 CAAAATTTCATAA-G-ATGTTAC
22607 CAAAATTTCATA
1 CAAAATTTCATA
22619 GGGAGAGAGG
Statistics
Matches: 115, Mismatches: 18, Indels: 21
0.75 0.12 0.14
Matches are distributed among these distances:
20 2 0.02
21 4 0.03
22 99 0.86
23 6 0.05
24 4 0.03
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (21 bp):
CAAAATTTCATAAGATGTTAC
Found at i:22590 original size:66 final size:66
Alignment explanation
Indices: 22449--22594 Score: 174
Period size: 66 Copynumber: 2.2 Consensus size: 66
22439 CATAGAAAAA
* * * *
22449 TTATCAAAATTTCATAGTATGATTACCAAAATTTCATATAGAGGTTATCAAAACTTCATAGTATA
1 TTATCAAAATTTCATAGTATGATTACCAAAATTTCATAAAAAGGTTACCAAAACTTCATAGGATA
22514 G
66 G
* *
22515 TTATCAAAATTTCATACAG-ATG-TTACCAAAATTTCATAAAAAGGTTACCAAAATTTCTTAGGG
1 TTATCAAAATTTCAT--AGTATGATTACCAAAATTTCATAAAAAGGTTACCAAAACTTCATA-GG
22578 AT-G
63 ATAG
22581 TTAAT-AAAATTTCA
1 TT-ATCAAAATTTCA
22595 AATGAAAGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
66 60 0.86
67 8 0.11
68 2 0.03
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (66 bp):
TTATCAAAATTTCATAGTATGATTACCAAAATTTCATAAAAAGGTTACCAAAACTTCATAGGATA
G
Found at i:22700 original size:22 final size:22
Alignment explanation
Indices: 22650--22719 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
22640 TGTGCTTATC
* **
22650 AAATTTCCTAGGGAGGTTAACA
1 AAATTTTCTAGGGAGGTTATGA
22672 AAATTTTCTAGGGAGGTTATGA
1 AAATTTTCTAGGGAGGTTATGA
*
22694 AAATTTTAT-GGAGAGGTTATCGA
1 AAATTTTCTAGG-GAGGTTAT-GA
22717 AAA
1 AAA
22720 GACATAGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 2 0.05
22 35 0.83
23 5 0.12
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (22 bp):
AAATTTTCTAGGGAGGTTATGA
Found at i:22795 original size:23 final size:22
Alignment explanation
Indices: 22758--22993 Score: 145
Period size: 22 Copynumber: 10.7 Consensus size: 22
22748 CTCATATGGA
*
22758 GGTTATCAAAATTTCATGGTGT
1 GGTTATCAAAATTTCATAGTGT
22780 GGTTATCAAAAATTTCATAGTGT
1 GGTTATC-AAAATTTCATAGTGT
* *
22803 GGTTA-C-CAATTTTATTTAGTGT
1 GGTTATCAAAATTTCA--TAGTGT
* * * *
22825 GATTATTAAAATTTTATAG-GCA
1 GGTTATCAAAATTTCATAGTG-T
* * * * *
22847 GATTATCAAAATCTCACACTGA
1 GGTTATCAAAATTTCATAGTGT
*
22869 GGTTATCGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* ** * *
22891 TGTTCCCAAAATTTCACAGTAT
1 GGTTATCAAAATTTCATAGTGT
* * * *
22913 GATTATCAAATTTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGT
* * **
22935 GGTTATCGAAATTTCATAATAA
1 GGTTATCAAAATTTCATAGTGT
* * *
22957 GGTTATCAAATTTTCAAAATGT
1 GGTTATCAAAATTTCATAGTGT
*
22979 GGTTATCAATATTTC
1 GGTTATCAAAATTTC
22994 TACATTGGAG
Statistics
Matches: 161, Mismatches: 46, Indels: 14
0.73 0.21 0.06
Matches are distributed among these distances:
20 6 0.04
21 1 0.01
22 127 0.79
23 20 0.12
24 7 0.04
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:23718 original size:2 final size:2
Alignment explanation
Indices: 23713--23747 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
23703 AGTGTGTGTG
*
23713 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23748 GCAACATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23804 original size:2 final size:2
Alignment explanation
Indices: 23797--23828 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23787 AAAATAACTA
23797 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
23829 ATATAAGGGT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:25628 original size:171 final size:172
Alignment explanation
Indices: 25246--25756 Score: 961
Period size: 171 Copynumber: 3.0 Consensus size: 172
25236 AGATTTGTCG
* *
25246 TTTACTACATAATTTACTCATCAACTCGTATAATTGGGCTTCAAGACAAAGATACGTTGGGTTTG
1 TTTACTACATACTCTACTCATCAACTCGTATAATTGGGCTTCAAGACAAAGATACGTTGGGTTTG
25311 TTTAGGAAAAGTGGATTGGGTAGGCTAGATATGAACCAGTCCAAGTCAATTAAAAACCATCAGCA
66 TTTAGGAAAAGTGGATTGGGTAGGCTAGATATGAACCAGTCCAAGTCAATTAAAAACCATCAGCA
25376 AATCATCTTGTCTTTGAACATCCTCCTTTCCCACAAGTCAGC
131 AATCATCTTGTCTTTGAACATCCTCCTTTCCCACAAGTCAGC
25418 TTTACTACATACTCTACTCATCAACTCGTATAATTGGGCTTCAAGACAAAGATACGTTGGGTTTG
1 TTTACTACATACTCTACTCATCAACTCGTATAATTGGGCTTCAAGACAAAGATACGTTGGGTTTG
25483 TTTAGGAAAAGTGGATTGGGTAGGCTAGATATGAACCAGTCCAAGTC-ATTAAAAACCATCAGCA
66 TTTAGGAAAAGTGGATTGGGTAGGCTAGATATGAACCAGTCCAAGTCAATTAAAAACCATCAGCA
25547 AATCATCTTGTCTTTGAACATCCTCCTTTCCCACAAGTCAGC
131 AATCATCTTGTCTTTGAACATCCTCCTTTCCCACAAGTCAGC
25589 TTTACTACATACTCTACTCATCAACTCGTATAATTGGGCTTCAAGACAAAGATACGTTGGGTTTG
1 TTTACTACATACTCTACTCATCAACTCGTATAATTGGGCTTCAAGACAAAGATACGTTGGGTTTG
* *
25654 TTTAGGAAAAGTGGATTGGGTAGGCCAGATATGAACCAGTCCAAGTCAATTAAAAACCGTCAGCA
66 TTTAGGAAAAGTGGATTGGGTAGGCTAGATATGAACCAGTCCAAGTCAATTAAAAACCATCAGCA
* *
25719 AATTATCTTGTCTTTGAACATTCTCCTTTCCCACAAGT
131 AATCATCTTGTCTTTGAACATCCTCCTTTCCCACAAGT
25757 TGCATCGTGT
Statistics
Matches: 332, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
171 170 0.51
172 162 0.49
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (172 bp):
TTTACTACATACTCTACTCATCAACTCGTATAATTGGGCTTCAAGACAAAGATACGTTGGGTTTG
TTTAGGAAAAGTGGATTGGGTAGGCTAGATATGAACCAGTCCAAGTCAATTAAAAACCATCAGCA
AATCATCTTGTCTTTGAACATCCTCCTTTCCCACAAGTCAGC
Found at i:28384 original size:13 final size:13
Alignment explanation
Indices: 28366--28390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28356 TTCAATGTTC
28366 TAAATATTATTTA
1 TAAATATTATTTA
28379 TAAATATTATTT
1 TAAATATTATTT
28391 GGAATTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:28429 original size:12 final size:10
Alignment explanation
Indices: 28400--28427 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
28390 TGGAATTCAA
28400 AATATATAAT
1 AATATATAAT
28410 AATATATAAT
1 AATATATAAT
28420 AATATATA
1 AATATATA
28428 TATTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATATATAAT
Found at i:32138 original size:2 final size:2
Alignment explanation
Indices: 32133--32165 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32123 TGTGTGTGTG
32133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32166 TGAATGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36022 original size:21 final size:20
Alignment explanation
Indices: 35990--36029 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
35980 TATTGTAAAT
* *
35990 TAAATAATAAACATTAAAAA
1 TAAATAAAAAACAATAAAAA
36010 TAAATAAAAAAACAATAAAA
1 TAAAT-AAAAAACAATAAAA
36030 TTTAAGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAATAAAAAACAATAAAAA
Found at i:36066 original size:25 final size:25
Alignment explanation
Indices: 36038--36091 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
36028 AATTTAAGAA
36038 ATAAATTAATATGAATCATGGTTGG
1 ATAAATTAATATGAATCATGGTTGG
**
36063 ATAAATTAATATGCCTCATGGTTGG
1 ATAAATTAATATGAATCATGGTTGG
36088 ATAA
1 ATAA
36092 TTGATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (25 bp):
ATAAATTAATATGAATCATGGTTGG
Found at i:36614 original size:9 final size:10
Alignment explanation
Indices: 36590--36615 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
36580 AAAGATTCTC
36590 ATTTTTTGGT
1 ATTTTTTGGT
36600 ATTTTTTGGT
1 ATTTTTTGGT
36610 ATTTTT
1 ATTTTT
36616 ATTGAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.73
Consensus pattern (10 bp):
ATTTTTTGGT
Found at i:39969 original size:22 final size:22
Alignment explanation
Indices: 39944--39990 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
39934 TTTCTGATTC
39944 GACCCCGA-AAAGGGTCGAACTG
1 GACCCCGAGAAA-GGTCGAACTG
* *
39966 GACCCTGAGGAAGGTCGAACTG
1 GACCCCGAGAAAGGTCGAACTG
39988 GAC
1 GAC
39991 AAGAGGAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.30, C:0.26, G:0.34, T:0.11
Consensus pattern (22 bp):
GACCCCGAGAAAGGTCGAACTG
Found at i:47440 original size:28 final size:28
Alignment explanation
Indices: 47400--47456 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
47390 TAACTATCCA
* *
47400 TTTTGGGACAAATTGACCCCTTAATTTT
1 TTTTGGGACAAATTGACCCATTAACTTT
*
47428 TTTTGGGACAAATTGGCCCATTAACTTT
1 TTTTGGGACAAATTGACCCATTAACTTT
47456 T
1 T
47457 AAAAACGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.42
Consensus pattern (28 bp):
TTTTGGGACAAATTGACCCATTAACTTT
Done.