Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009778.1 Corchorus capsularis cultivar CVL-1 contig09799, 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: 37533
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:470 original size:17 final size:17
Alignment explanation
Indices: 448--509 Score: 79
Period size: 17 Copynumber: 3.4 Consensus size: 17
438 CTAGTATATA
448 TATATATATCTATACTG
1 TATATATATCTATACTG
465 TATATATATCTATACTG
1 TATATATATCTATACTG
482 TATTGAAAATATATCTATACTG
1 TA-T----ATATATCTATACTG
504 TATATA
1 TATATA
510 AAAGTACGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 22 0.55
18 1 0.03
21 1 0.03
22 16 0.40
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (17 bp):
TATATATATCTATACTG
Found at i:579 original size:31 final size:31
Alignment explanation
Indices: 544--602 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
534 ATGTTTTTTG
544 ATTGTATCCATATT-TTTAAAACATATTTTCA
1 ATTGTA-CCATATTCTTTAAAACATATTTTCA
*
575 ATTGTACCATTTTCTTTAAAACATATTT
1 ATTGTACCATATTCTTTAAAACATATTT
603 CTAAATTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTGTACCATATTCTTTAAAACATATTTTCA
Found at i:767 original size:38 final size:35
Alignment explanation
Indices: 703--779 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 35
693 AATTTGCCTT
*
703 TTTGTTTCCAACGTCCTATTTAATTTTGTCTTTTGTC
1 TTTGTTTCCAACGTCATATTTAATTTTG-C-TTTGTC
*
740 TTTGTTTCCAATCGTTATATTTAATTTTGCTTTGTC
1 TTTGTTTCCAA-CGTCATATTTAATTTTGCTTTGTC
776 TTTG
1 TTTG
780 GTCCTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 12 0.32
38 15 0.41
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.58
Consensus pattern (35 bp):
TTTGTTTCCAACGTCATATTTAATTTTGCTTTGTC
Found at i:939 original size:19 final size:21
Alignment explanation
Indices: 907--949 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
897 TTCTTTACTA
907 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
928 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
947 TTA
1 TTA
950 AATATCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:1189 original size:22 final size:22
Alignment explanation
Indices: 1117--1262 Score: 89
Period size: 22 Copynumber: 6.4 Consensus size: 22
1107 CTTGTCTCTA
*
1117 TGTGGTTATCAAAATTTCATAA
1 TGTGGTTATCAAAATTTCATAG
** * *
1139 AATGGTTATTATAATTTCATGAG
1 TGTGGTTATCAAAATTTCAT-AG
*
1162 -GAGGTTATCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
* *
1183 TGTGGTTACCGAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
* * *
1205 -GATCAGGTTATTAAAATATCTTAGG
1 TG-T--GGTTATCAAAATTTCATA-G
*
1230 TTGGTAGGTTATTAAAATTTCATAG
1 -T-GT-GGTTATCAAAATTTCATAG
*
1255 GGTGGTTA
1 TGTGGTTA
1263 ATTATCACAA
Statistics
Matches: 95, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
21 3 0.03
22 55 0.58
23 3 0.03
24 13 0.14
25 2 0.02
26 17 0.18
27 1 0.01
28 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.39
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCATAG
Found at i:1199 original size:44 final size:43
Alignment explanation
Indices: 1120--1206 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 43
1110 GTCTCTATGT
**
1120 GGTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCATAAAATGGTTACGATAATTTCAT-AGGA
***
1164 GGTTATCAAAATTTCATAGTGTGGTTACCGA-AATTTCATAGGA
1 GGTTATCAAAATTTCATAAAATGGTTA-CGATAATTTCATAGGA
1207 TCAGGTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 4 0.11
44 32 0.86
45 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAAAATGGTTACGATAATTTCATAGGA
Found at i:1255 original size:26 final size:26
Alignment explanation
Indices: 1209--1260 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1199 TCATAGGATC
* *
1209 AGGTTATTAAAATATCTTAGGTTGGT
1 AGGTTATTAAAATATCATAGGGTGGT
*
1235 AGGTTATTAAAATTTCATAGGGTGGT
1 AGGTTATTAAAATATCATAGGGTGGT
1261 TAATTATCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.25, T:0.40
Consensus pattern (26 bp):
AGGTTATTAAAATATCATAGGGTGGT
Found at i:1421 original size:22 final size:21
Alignment explanation
Indices: 1373--1657 Score: 125
Period size: 22 Copynumber: 12.8 Consensus size: 21
1363 TTTCATGGGG
* *
1373 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
1395 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
1417 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
1442 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
1464 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
1483 AGTGATTATCAAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
1506 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
* *
1531 AGATTATCAAAATTCCATAG-
1 AGGTTATCAAAATTTCATAGA
* *
1551 TGTTGTTATCAAAATTACATA-A
1 AG--GTTATCAAAATTTCATAGA
* *
1573 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * *
1596 GGGGTCAACAAAATTTTATA-A
1 -AGGTTATCAAAATTTCATAGA
*
1617 AGAGTTTATCAAAATTTCATAAA
1 AG-G-TTATCAAAATTTCATAGA
*
1640 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
1658 AAATGTGATT
Statistics
Matches: 203, Mismatches: 33, Indels: 54
0.70 0.11 0.19
Matches are distributed among these distances:
19 2 0.01
20 12 0.06
21 27 0.13
22 115 0.57
23 7 0.03
24 9 0.04
25 21 0.10
26 6 0.03
27 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:1520 original size:46 final size:43
Alignment explanation
Indices: 1450--1682 Score: 161
Period size: 44 Copynumber: 5.3 Consensus size: 43
1440 TAAGGAGTAC
* *
1450 CAAAATTTGATAGA-AGGTTATC-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGTGGTTATCAAAAT-TCATAGAGTGATTAT
* **
1492 CAAAATTTCATAGAGATCGGATTATCAAAATTTATAGAAAGATTAT
1 CAAAATTTCATAGAG-T-GG-TTATCAAAATTCATAGAGTGATTAT
* * *
1538 CAAAATTCCATAGTGTTGTTATCAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGAGTGGTTATCAAAATT-CATAGA-GTGATTAT
* * * * * * * *
1582 CAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGTTTAT
1 CAAAATTTCATAGAGTGGTTATCAAAA-TTCATAGAGTGATTAT
* * * *
1626 CAAAATTTCATAAAGAGGTTATCAAATTTTCA-AAATGTGATTA-
1 CAAAATTTCATAGAGTGGTTATCAAA-ATTCATAGA-GTGATTAT
1669 CAAAAATTTCATAG
1 C-AAAATTTCATAG
1683 TGATATTTCT
Statistics
Matches: 148, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
42 13 0.09
43 16 0.11
44 79 0.53
45 6 0.04
46 30 0.20
47 4 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (43 bp):
CAAAATTTCATAGAGTGGTTATCAAAATTCATAGAGTGATTAT
Found at i:1630 original size:88 final size:88
Alignment explanation
Indices: 1484--1682 Score: 215
Period size: 88 Copynumber: 2.2 Consensus size: 88
1474 ATCTCATAGA
* *
1484 GTGATTATCAAAATTTCATAGAGATCGGATTATCAAAATTTATAGAAAGATTATCAAAATTCCAT
1 GTGATTATCAAAATTTCATAGAGA--GGATCAACAAAATTTATAGAAAGATTATCAAAATTCCAT
** ** *
1549 AGTGTTGTTATCAAAATTACATAAT
64 AAAGAGGTTATCAAAATTACAAAAT
* * * *
1574 GTGATTATCAGAATTTCATAGAG-GGGTCAACAAAATTTTATA-AAGAGTTTATCAAAATTTCAT
1 GTGATTATCAAAATTTCATAGAGAGGATCAACAAAA-TTTATAGAA-AGATTATCAAAATTCCAT
* *
1637 AAAGAGGTTATCAAATTTTCAAAAT
64 AAAGAGGTTATCAAAATTACAAAAT
1662 GTGATTA-CAAAAATTTCATAG
1 GTGATTATC-AAAATTTCATAG
1683 TGATATTTCT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
87 12 0.13
88 58 0.63
90 22 0.24
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (88 bp):
GTGATTATCAAAATTTCATAGAGAGGATCAACAAAATTTATAGAAAGATTATCAAAATTCCATAA
AGAGGTTATCAAAATTACAAAAT
Found at i:1872 original size:22 final size:21
Alignment explanation
Indices: 1763--1965 Score: 78
Period size: 22 Copynumber: 9.5 Consensus size: 21
1753 TTATGGAGTA
* * *
1763 ATCAAGATTTCA-ATGAGGAT
1 ATCAAAATTTCACAAGAGGTT
** *
1783 ATCAAAA-TTCA-GGGAGGAT
1 ATCAAAATTTCACAAGAGGTT
1802 ATCAAAATTTCATACAA-AGGTT
1 ATCAAAATTTC--ACAAGAGGTT
1824 ATCAAAATTTCAC-AGTTTA-GTT
1 ATCAAAATTTCACAAG---AGGTT
*
1846 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCACAAGA-GGTT
* * *
1868 ATCAAAATTTCA-TAGTATGTAG
1 ATCAAAATTTCACAAG-AGGT-T
* * *
1890 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCACA-AGAGGTT
* * *
1912 AACAAAATTTCATAATGAGATT
1 ATCAAAATTTCACAA-GAGGTT
** * *
1934 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCACA-AGAGGTT
1956 ATCAAAATTT
1 ATCAAAATTT
1966 GTAGTTATCA
Statistics
Matches: 141, Mismatches: 25, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
19 18 0.13
20 12 0.09
21 4 0.03
22 101 0.72
23 5 0.04
24 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (21 bp):
ATCAAAATTTCACAAGAGGTT
Found at i:1938 original size:44 final size:44
Alignment explanation
Indices: 1801--2312 Score: 248
Period size: 44 Copynumber: 11.8 Consensus size: 44
1791 TCAGGGAGGA
*** * * *
1801 TATCAAAATTTCATACAAAGGTTATCAAAATTTCACAGTTTAG-T
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAG-TGAGAT
* *
1845 TTTCAAAATTTCACAAGAGG-G-TTATCAAAATTTCATAGT-ATG-T
1 TATCAAAATTTCA-TAG-GGAGATTATCAAAATTTCATAGTGA-GAT
* * *
1888 AGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGAT
1 -TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGAT
** *
1933 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GT-AG-T
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGAT
* *
1971 TATCAAGAA-ATCATAGGGAGGTTATCAAAA-TT--T-GT-AG-T
1 TATCAA-AATTTCATAGGGAGATTATCAAAATTTCATAGTGAGAT
* * * *
2009 TATCAAGATTTCATA-AGAAAGTTATCAAAATTTCATAGGGAGATT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGA-T
* * *
2054 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGA-AGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGA-T
* * * * *
2099 TATCACAATTTCATAGTGTGATTATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGAT
* * * * *
2143 TA-CTAACAA-TTCGTATGGAGATTTTTAAATTTTCATAACGTG-G-T
1 TATC-AA-AATTTCATAGGGAGATTATCAAAATTTCAT-A-GTGAGAT
* * * * * * * *
2187 TATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG-AGAT
* * *
2232 TATCAAAATTTCATTGGGA-AGTTATCAAAATTTCATATTGAGGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGAT
* * * * *
2276 CT-TCAAAATTCCTTAGGGAGGTTAACCAAATTTCATA
1 -TATCAAAATTTCATAGGGAGATTATCAAAATTTCATA
2313 AGAAGGTTAA
Statistics
Matches: 364, Mismatches: 72, Indels: 64
0.73 0.14 0.13
Matches are distributed among these distances:
37 3 0.01
38 56 0.15
39 6 0.02
40 1 0.00
41 2 0.01
42 7 0.02
43 13 0.04
44 177 0.49
45 75 0.21
46 24 0.07
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (44 bp):
TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGAT
Found at i:1974 original size:16 final size:16
Alignment explanation
Indices: 1953--2019 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 16
1943 TCATAGGGAG
1953 GTTATCAAAATTTGTA
1 GTTATCAAAATTTGTA
* *
1969 GTTATCAAGAAATCATAGGGA
1 GTTATC-A-AAAT--T-TGTA
1990 GGTTATCAAAATTTGTA
1 -GTTATCAAAATTTGTA
*
2007 GTTATCAAGATTT
1 GTTATCAAAATTT
2020 CATAAGAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
16 18 0.45
17 3 0.08
18 5 0.12
20 5 0.12
21 3 0.08
22 6 0.15
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.37
Consensus pattern (16 bp):
GTTATCAAAATTTGTA
Found at i:1983 original size:38 final size:38
Alignment explanation
Indices: 1932--2041 Score: 166
Period size: 38 Copynumber: 2.9 Consensus size: 38
1922 CATAATGAGA
*
1932 TTATCAAAAAATCATAGGGAGGTTATCAAAATTTGTAG
1 TTATCAAGAAATCATAGGGAGGTTATCAAAATTTGTAG
1970 TTATCAAGAAATCATAGGGAGGTTATCAAAATTTGTAG
1 TTATCAAGAAATCATAGGGAGGTTATCAAAATTTGTAG
** * * *
2008 TTATCAAGATTTCATAAGAAAGTTATCAAAATTT
1 TTATCAAGAAATCATAGGGAGGTTATCAAAATTT
2042 CATAGGGAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (38 bp):
TTATCAAGAAATCATAGGGAGGTTATCAAAATTTGTAG
Found at i:2114 original size:22 final size:21
Alignment explanation
Indices: 1801--2397 Score: 161
Period size: 22 Copynumber: 27.6 Consensus size: 21
1791 TCAGGGAGGA
**
1801 TATCAAAATTTCATACAAAGGT
1 TATCAAAATTTCATAGGAA-GT
* **
1823 TATCAAAATTTCACAGTTTAGT
1 TATCAAAATTTCATAG-GAAGT
* * * *
1845 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATAGGA-AGT
* *
1867 TATCAAAATTTCATAGTATGT
1 TATCAAAATTTCATAGGAAGT
* *
1888 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGGAAG-T
* *
1911 TAACAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-AGGAAG-T
** *
1933 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATA-GGAAGT
*
1955 TATCAAAA-TT--T--GTAGT
1 TATCAAAATTTCATAGGAAGT
* *
1971 TATCAAGAA-ATCATAGGGAGGT
1 TATCAA-AATTTCATA-GGAAGT
*
1993 TATCAAAA-TT--T--GTAGT
1 TATCAAAATTTCATAGGAAGT
* *
2009 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCAT-AGGAAGT
*
2031 TATCAAAATTTCATAGGGAGATT
1 TATCAAAATTTCATA-GGA-AGT
*
2054 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGGAAG--T
2077 TATCAAAATTTCATAGCGAAGT
1 TATCAAAATTTCATAG-GAAGT
* *
2099 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATAG-GAAG-T
* *
2121 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATAG-GAAG-T
*
2143 TA-CTAACAA-TTCGTATGG-AGAT
1 TATC-AA-AATTTCATA-GGAAG-T
* * * * **
2165 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCAT-AGGAAGT
* * *
2187 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATA-GGAAGT
* * **
2209 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAG-G-AAGT
*
2232 TATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCA-TAGGAAGT
* *
2254 TATCAAAATTTCATATTGAGGT
1 TATCAAAATTTCATA-GGAAGT
* * *
2276 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATA-GGAAGT
* * *
2298 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATAGGAA-GT
** **
2320 TAAAAAAAATTT-ATAAAAAGGT
1 T-ATCAAAATTTCATAGGAA-GT
* * * * *
2342 TCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGA-AGT
*
2364 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATAGGAA-GT
2386 TATCAAAATTTC
1 TATCAAAATTTC
2398 CTAATAGGAT
Statistics
Matches: 427, Mismatches: 104, Indels: 88
0.69 0.17 0.14
Matches are distributed among these distances:
16 19 0.04
17 5 0.01
19 4 0.01
21 23 0.05
22 304 0.71
23 66 0.15
24 6 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (21 bp):
TATCAAAATTTCATAGGAAGT
Found at i:2256 original size:45 final size:45
Alignment explanation
Indices: 2183--2268 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
2173 TTTCATAACG
* * *
2183 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
2228 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
2269 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:2528 original size:2 final size:2
Alignment explanation
Indices: 2521--2555 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2511 CTAAAACTAG
*
2521 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2556 ACGACCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5266 original size:23 final size:23
Alignment explanation
Indices: 5239--5292 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
5229 AGATGCTAAT
*
5239 ATATACTGT-GACTTGGCTAAAAA
1 ATATA-TGTAGACTTGGATAAAAA
* *
5262 ATATATGTAGATTTGGATAAAAC
1 ATATATGTAGACTTGGATAAAAA
*
5285 ATAAATGT
1 ATATATGT
5293 GTTTGTTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (23 bp):
ATATATGTAGACTTGGATAAAAA
Found at i:5700 original size:31 final size:30
Alignment explanation
Indices: 5665--5723 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
5655 TTGTAAGGAC
*
5665 TGATTTGAGCCGATTTTGCAACGTTAGGGAT
1 TGATTTGAG-CAATTTTGCAACGTTAGGGAT
* *
5696 TGATTTGAGTAATTTTGTAACGTTAGGG
1 TGATTTGAGCAATTTTGCAACGTTAGGG
5724 GCTTAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (30 bp):
TGATTTGAGCAATTTTGCAACGTTAGGGAT
Found at i:8170 original size:20 final size:21
Alignment explanation
Indices: 8132--8170 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8122 TTTCTTTTAT
8132 TATCATTTTTTTTCTATTGAA
1 TATCATTTTTTTTCTATTGAA
8153 TATCATTTTTTTTC-ATTG
1 TATCATTTTTTTTCTATTG
8171 TTGTTCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (21 bp):
TATCATTTTTTTTCTATTGAA
Found at i:9593 original size:27 final size:27
Alignment explanation
Indices: 9555--9608 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9545 TTTCACAACA
9555 AAATTTCATTTCTTAACTGAATTTTCT
1 AAATTTCATTTCTTAACTGAATTTTCT
9582 AAATTTCATTTCTTAACTGAATTTTCT
1 AAATTTCATTTCTTAACTGAATTTTCT
9609 TAAAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.52
Consensus pattern (27 bp):
AAATTTCATTTCTTAACTGAATTTTCT
Found at i:9607 original size:14 final size:14
Alignment explanation
Indices: 9563--9611 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
9553 CAAAATTTCA
9563 TTTCTTAACTGAAT
1 TTTCTTAACTGAAT
* * **
9577 TTTCTAAATTTCA-
1 TTTCTTAACTGAAT
9590 TTTCTTAACTGAAT
1 TTTCTTAACTGAAT
9604 TTTCTTAA
1 TTTCTTAA
9612 AATAATTTAT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (14 bp):
TTTCTTAACTGAAT
Found at i:9619 original size:27 final size:27
Alignment explanation
Indices: 9562--9619 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
9552 ACAAAATTTC
* *
9562 ATTTCTTAACTGAATTTTCTAAATTTC
1 ATTTCTTAACTGAATTTTCTAAATATA
9589 ATTTCTTAACTGAATTTTCTTAAA-ATA
1 ATTTCTTAACTGAATTTTC-TAAATATA
9616 ATTT
1 ATTT
9620 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (27 bp):
ATTTCTTAACTGAATTTTCTAAATATA
Found at i:9874 original size:17 final size:17
Alignment explanation
Indices: 9852--9884 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9842 ATAATTTCTC
9852 CAAACAAATCAATTAAT
1 CAAACAAATCAATTAAT
*
9869 CAAACAAATTAATTAA
1 CAAACAAATCAATTAA
9885 GAAAGTCTAC
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:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
CAAACAAATCAATTAAT
Found at i:13163 original size:54 final size:55
Alignment explanation
Indices: 13073--13181 Score: 152
Period size: 54 Copynumber: 2.0 Consensus size: 55
13063 TCCTTTATTT
* * *
13073 TTTGAATTATATTATTTTTGAAATCCTAATTCAAACATCAAAA-TGAATGGACGAG
1 TTTGAATTATATTATTTCTGAAATCCCAATTCAAACACCAAAATTG-ATGGACGAG
13128 TTTGAATTGA-ATTATTTCTG-AATCCCAATTCAAACACCAAAATTGATGGACGAG
1 TTTGAATT-ATATTATTTCTGAAATCCCAATTCAAACACCAAAATTGATGGACGAG
13182 AATGATTACC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
54 29 0.59
55 19 0.39
56 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (55 bp):
TTTGAATTATATTATTTCTGAAATCCCAATTCAAACACCAAAATTGATGGACGAG
Found at i:14414 original size:87 final size:86
Alignment explanation
Indices: 14301--14506 Score: 238
Period size: 87 Copynumber: 2.4 Consensus size: 86
14291 CAGGCACAAA
* *
14301 ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCATCATTACTAACCAAAACTCCATTCA-GAAGA
1 ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACTAACCAAAACTCCATT-AGGAAGA
14365 TCACTAA-AATTTGAATTCAAACT
65 TCAC-AACAA-TTGAATTCAAACT
* * * *
14388 ATCCTCTACCATAAT-ATTTTCCAAAGATTTTGCACCATAACTACCCATAACTCCATTAGGAAGA
1 ATCCTCCACCA-AATCAGTTTCCAAAGATTTTGCACCATAACTAACCAAAACTCCATTAGGAAGA
*
14452 TCACAATCAATTGAATTCAAATT
65 TCACAA-CAATTGAATTCAAACT
* ** * *
14475 ATTCTCCACCTTATCAGTTTCCACAGAATTTG
1 ATCCTCCACCAAATCAGTTTCCAAAGATTTTG
14507 TGCTTAAAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
86 5 0.05
87 90 0.90
88 5 0.05
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (86 bp):
ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACTAACCAAAACTCCATTAGGAAGAT
CACAACAATTGAATTCAAACT
Found at i:23422 original size:2 final size:2
Alignment explanation
Indices: 23415--23439 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23405 TAACATATTT
23415 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 T
23440 GTGTGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28699 original size:157 final size:156
Alignment explanation
Indices: 28284--28686 Score: 514
Period size: 157 Copynumber: 2.6 Consensus size: 156
28274 CATCTTGGCT
* * *
28284 AAGTTTCATTTTCAAACGGACTTAGAATGAAAAACTTATGCACGTTTTTTCATTTAAGGACAGTT
1 AAGTTTCA-TCTCAATCGGACTTAGAATGAAAAACTTATGCATG-TTTTTCATTTAAGGACAGTT
** * * *
28349 TGGGGTAAGAAAACTAGTTCACCATCAAGGATAGCTCGATTTTACTTAGAATTTTTTCCATAGTT
64 TGGGGTGTGAAACCTAGTTCACCATCAAGGACAGCTCGATTTTACTTAGAATTTTTTCCATAGTC
28414 TTATGGAGATAATCTAAGCATACTGGTGGA
129 TTATGGAGATAATCTAAGCA-ACT-GTGGA
* * *
28444 AA--TTCAGC-CTTATTGGACTTA-AGATGAAAAACTTATGC-TAGTTTTTCATTTAAGGACAGT
1 AAGTTTCATCTC-AATCGGACTTAGA-ATGAAAAACTTATGCAT-GTTTTTCATTTAAGGACAGT
*
28504 TTGGGGTGTGAAACCTAGTTCACCATCAAGGACAGCTCGGTTTTACTTAGGAATTTTTTCCATAG
63 TTGGGGTGTGAAACCTAGTTCACCATCAAGGACAGCTCGATTTTACTTA-GAATTTTTTCCATAG
* * *
28569 TCTTATTGAGATATTCTAAGTC-CCT-TGGAA
127 TCTTATGGAGATAATCTAAG-CAACTGTGG-A
*
28599 AAGTTTCATCTCAATCAGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTG
1 AAGTTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTG
*
28664 AGGTGTGAAACCTAGTTCACCAT
66 GGGTGTGAAACCTAGTTCACCAT
28687 GAAGAAGGGC
Statistics
Matches: 212, Mismatches: 20, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
154 3 0.01
155 3 0.01
156 67 0.32
157 129 0.61
158 8 0.04
160 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (156 bp):
AAGTTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTG
GGGTGTGAAACCTAGTTCACCATCAAGGACAGCTCGATTTTACTTAGAATTTTTTCCATAGTCTT
ATGGAGATAATCTAAGCAACTGTGGA
Found at i:29049 original size:28 final size:28
Alignment explanation
Indices: 29007--29078 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
28997 GCATGCCATG
* *
29007 TGATACATCAGAGGGACGATTTTACGCC
1 TGATACATCAGAGGGACAATTTCACGCC
* *
29035 TGATACATCATAGGGACAATTTCATGCC
1 TGATACATCAGAGGGACAATTTCACGCC
*
29063 TGGTACATCAGAGGGA
1 TGATACATCAGAGGGA
29079 GACATCCTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (28 bp):
TGATACATCAGAGGGACAATTTCACGCC
Found at i:30469 original size:5 final size:5
Alignment explanation
Indices: 30459--30501 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
30449 GGGAGACTTC
30459 TTTCT TTTCT TTTCT TTTCT TTTCT ATTT-T TTT-T TTT-T TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT -TTTCT TTTCT TTTCT TTTCT
30502 AATTTTTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 11 0.31
5 22 0.61
6 3 0.08
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTCT
Found at i:30494 original size:18 final size:19
Alignment explanation
Indices: 30468--30508 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
30458 CTTTCTTTTC
30468 TTTTCTTTTCTTTTCT-AT
1 TTTTCTTTTCTTTTCTAAT
* *
30486 TTTTTTTTTTTTTTCTAAT
1 TTTTCTTTTCTTTTCTAAT
30505 TTTT
1 TTTT
30509 GCAGTATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTCTTTTCTTTTCTAAT
Found at i:32465 original size:46 final size:46
Alignment explanation
Indices: 32398--32489 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
32388 TTTCATGATG
32398 GAGAAAGTGGAAATTACTTATTAGTTGTTACTGAGTGATCATTTTA
1 GAGAAAGTGGAAATTACTTATTAGTTGTTACTGAGTGATCATTTTA
32444 GAGAAAGTGGAAATTACTTATTAGTTGTTACTGAGTGATCATTTTA
1 GAGAAAGTGGAAATTACTTATTAGTTGTTACTGAGTGATCATTTTA
32490 TTTTAATCGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.39
Consensus pattern (46 bp):
GAGAAAGTGGAAATTACTTATTAGTTGTTACTGAGTGATCATTTTA
Found at i:34220 original size:17 final size:17
Alignment explanation
Indices: 34198--34234 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
34188 GTTATCCAGC
34198 ACCTCATGATACCTAGT
1 ACCTCATGATACCTAGT
*
34215 ACCTCATGCTACCTAGT
1 ACCTCATGATACCTAGT
34232 ACC
1 ACC
34235 ATGAGGGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (17 bp):
ACCTCATGATACCTAGT
Done.