Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007463.1 Corchorus capsularis cultivar CVL-1 contig07484, 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: 22692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:196 original size:14 final size:14
Alignment explanation
Indices: 177--203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
167 CTGCAAAAAA
177 TTATAGGCTCACTG
1 TTATAGGCTCACTG
191 TTATAGGCTCACT
1 TTATAGGCTCACT
204 TTTGCTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATAGGCTCACTG
Found at i:1232 original size:29 final size:28
Alignment explanation
Indices: 1175--1254 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 28
1165 TACTGATTAC
*
1175 CATTTTTAC-TTTTTC-TACT-TTTAT-
1 CATTTTTACTTTTTTCTTACTCTTTTTA
1199 CATTTTTACTTTTTTCTTACTCTTTTTA
1 CATTTTTACTTTTTTCTTACTCTTTTTA
* *
1227 C-TATTTACTCTTTTCTTACTCTCTTTTA
1 CATTTTTACTTTTTTCTTACTCT-TTTTA
1255 TTGATTACCA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 9 0.19
25 6 0.12
26 4 0.08
27 23 0.48
28 6 0.12
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (28 bp):
CATTTTTACTTTTTTCTTACTCTTTTTA
Found at i:1268 original size:29 final size:27
Alignment explanation
Indices: 1210--1279 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
1200 ATTTTTACTT
*
1210 TTTTCTTACTCTTTTTACTATTTACTC
1 TTTTCTTACTCTTTTTACTATTTACAC
*
1237 TTTTCTTACTCTCTTTTATTGA-TTACCAC
1 TTTTCTTACTCT-TTTTACT-ATTTA-CAC
1266 -TTT-TTACTCTTTTT
1 TTTTCTTACTCTTTTT
1280 TTTCTTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 4 0.11
27 19 0.50
28 12 0.32
29 3 0.08
ACGTcount: A:0.14, C:0.21, G:0.01, T:0.63
Consensus pattern (27 bp):
TTTTCTTACTCTTTTTACTATTTACAC
Found at i:1325 original size:25 final size:22
Alignment explanation
Indices: 1282--1533 Score: 226
Period size: 22 Copynumber: 11.8 Consensus size: 22
1272 CTCTTTTTTT
*
1282 TCTTATACTGACTACCATTTTAC
1 TCTT-TACTGATTACCATTTTAC
*
1305 TCTTTGAATTTGATTACCATTTTAC
1 TCTTT--A-CTGATTACCATTTTAC
* *
1330 TATTTACTGATTACTATTTTAC
1 TCTTTACTGATTACCATTTTAC
* *
1352 TC-TTACTAATTACCATTTTGC
1 TCTTTACTGATTACCATTTTAC
*
1373 TC-TTACTGATTACTATTTTAC
1 TCTTTACTGATTACCATTTTAC
1394 TC-TTACTGATTACC-TTTTA-
1 TCTTTACTGATTACCATTTTAC
*
1413 ------CTGATTACTATTTTAC
1 TCTTTACTGATTACCATTTTAC
1429 TCTTTACTGATTACC-TTCTTAC
1 TCTTTACTGATTACCATT-TTAC
* * *
1451 TTTTTACTGATTACTATTTCAC
1 TCTTTACTGATTACCATTTTAC
*
1473 TCTTTACTGATTACCATTTTGC
1 TCTTTACTGATTACCATTTTAC
*
1495 TC-TTACTGATTACTATTTTAC
1 TCTTTACTGATTACCATTTTAC
*
1516 -CTTTTACTGATTATCATT
1 TC-TTTACTGATTACCATT
1534 ACTTTTTTAC
Statistics
Matches: 188, Mismatches: 26, Indels: 31
0.77 0.11 0.13
Matches are distributed among these distances:
14 8 0.04
15 5 0.03
20 6 0.03
21 66 0.35
22 77 0.41
23 7 0.04
24 1 0.01
25 18 0.10
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (22 bp):
TCTTTACTGATTACCATTTTAC
Found at i:1544 original size:43 final size:43
Alignment explanation
Indices: 1408--1571 Score: 160
Period size: 43 Copynumber: 3.8 Consensus size: 43
1398 ACTGATTACC
1408 TTTTACTGATTACTATTTTACTCTTTACTGATTACCTTC-TTAC-T
1 TTTTACTGATTACTATTTTACTCTTTACTGATTA---TCATTACTT
* *
1452 TTTTACTGATTACTATTTCACTCTTTACTGATTACCATT--TT
1 TTTTACTGATTACTATTTTACTCTTTACTGATTATCATTACTT
*
1493 GCTCTTACTGATTACTATTTTAC-CTTTTACTGATTATCATTACTT
1 --TTTTACTGATTACTATTTTACTC-TTTACTGATTATCATTACTT
** * *
1538 TTTTACTCTTTACTGATTAT-CTTTTTACTGATTA
1 TTTTACTGATTACT-ATTTTACTCTTTACTGATTA
1572 CCCTTTACTC
Statistics
Matches: 101, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
43 57 0.56
44 37 0.37
45 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.54
Consensus pattern (43 bp):
TTTTACTGATTACTATTTTACTCTTTACTGATTATCATTACTT
Found at i:1557 original size:28 final size:28
Alignment explanation
Indices: 1503--1558 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1493 GCTCTTACTG
1503 ATTACTATTTTACCTTTTACTGATTATC
1 ATTACTATTTTACCTTTTACTGATTATC
*
1531 ATTACTTTTTTA-CTCTTTACTGATTATC
1 ATTACTATTTTACCT-TTTACTGATTATC
1559 TTTTTACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.23, C:0.18, G:0.04, T:0.55
Consensus pattern (28 bp):
ATTACTATTTTACCTTTTACTGATTATC
Found at i:1572 original size:22 final size:22
Alignment explanation
Indices: 1408--1572 Score: 121
Period size: 22 Copynumber: 7.6 Consensus size: 22
1398 ACTGATTACC
*
1408 TTTTACTGATTACTATTTTACT
1 TTTTACTGATTACTATTATACT
*
1430 CTTTACTGATTACCT-TCT-TACT
1 TTTTACTGATTA-CTAT-TATACT
1452 TTTTACTGATTACTATT-TCACT
1 TTTTACTGATTACTATTAT-ACT
* * * *
1474 CTTTACTGATTACCATTTTGC-
1 TTTTACTGATTACTATTATACT
* * *
1495 TCTTACTGATTACTATTTTACC
1 TTTTACTGATTACTATTATACT
1517 TTTTACTGATTA-TCA-T-TACTT
1 TTTTACTGATTACT-ATTATAC-T
**
1538 TTTTACTCTTTACTGATTAT-CT
1 TTTTACTGATTACT-ATTATACT
1560 TTTTACTGATTAC
1 TTTTACTGATTAC
1573 CCTTTACTCT
Statistics
Matches: 116, Mismatches: 16, Indels: 22
0.75 0.10 0.14
Matches are distributed among these distances:
20 3 0.03
21 33 0.28
22 73 0.63
23 6 0.05
24 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTTACTGATTACTATTATACT
Found at i:1628 original size:35 final size:35
Alignment explanation
Indices: 1561--1659 Score: 146
Period size: 35 Copynumber: 2.9 Consensus size: 35
1551 TGATTATCTT
* *
1561 TTTACTGATTACCCTTTAC-TCTTACCATTCTTCC
1 TTTACTGATTACTCTTTACTTTTTACCATTCTTCC
*
1595 TTTACTGATTACTCTTTACTTTTTACCATTCTTCT
1 TTTACTGATTACTCTTTACTTTTTACCATTCTTCC
* *
1630 TTTATTGATTACTCTTTACTCTTTACCATT
1 TTTACTGATTACTCTTTACTTTTTACCATT
1660 TTACTCTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
34 18 0.31
35 41 0.69
ACGTcount: A:0.18, C:0.25, G:0.03, T:0.54
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTTTTTACCATTCTTCC
Found at i:1835 original size:32 final size:32
Alignment explanation
Indices: 1774--1859 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 32
1764 TTCTTAATTA
*
1774 TTAATTTACTGATTAGTCCTTTTTTACTTCCTTTC
1 TTAA-TTACTGATTAAT-C-TTTTTACTTCCTTTC
* *
1809 TTAGTTACTGATTAATCTTTTTACTTCTTTTC
1 TTAATTACTGATTAATCTTTTTACTTCCTTTC
*
1841 TTAATTACTGATTACTCTT
1 TTAATTACTGATTAATCTT
1860 CTACTCTCTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 31 0.67
33 1 0.02
34 11 0.24
35 3 0.07
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.57
Consensus pattern (32 bp):
TTAATTACTGATTAATCTTTTTACTTCCTTTC
Found at i:1848 original size:105 final size:104
Alignment explanation
Indices: 1732--1999 Score: 229
Period size: 105 Copynumber: 2.5 Consensus size: 104
1722 TCTTACTTTG
* * *
1732 ACTCTCAATTACCAATTTTACTGATTAATCCCTTCTTAATTATTAATTTACTGATTAGT-CCTTT
1 ACTCTTAATTACCAATTTTACTGATTAATCCCTTCTTAATTATTAATTTACTGATTAATCCCTTG
** ** * * *
1796 TTTACTTCCTTTCTTAGTTACTGATTAATCTTTTTACTTCTT
66 ACT-CTTAATTACTGAGTTACTGATTAATATTTTTAC--CTT
* ** ** * * * * *
1838 -TTCTTAATTACTGA--TTACTCTTCTACTCTCTCCCTTAAGTATCAATTTACTGATTAATCCCT
1 ACTCTTAATTACCAATTTTACTGAT-TAATCCCT-TCTTAATTATTAATTTACTGATTAATCCCT
* *
1900 TGACTCTTAATTACTGATTTACTGATTACTATTTTTACCTT
64 TGACTCTTAATTACTGAGTTACTGATTAATATTTTTACCTT
* *
1941 GACTCTTGATTATCAATTTTACTGATTAATCCCTTCTTAATTATTAATTTTACTGATTA
1 -ACTCTTAATTACCAATTTTACTGATTAATCCCTTCTTAATTATTAA-TTTACTGATTA
2000 CTATTACTTT
Statistics
Matches: 120, Mismatches: 34, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
103 9 0.08
104 6 0.05
105 77 0.64
106 22 0.18
107 6 0.05
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.50
Consensus pattern (104 bp):
ACTCTTAATTACCAATTTTACTGATTAATCCCTTCTTAATTATTAATTTACTGATTAATCCCTTG
ACTCTTAATTACTGAGTTACTGATTAATATTTTTACCTT
Found at i:1909 original size:34 final size:34
Alignment explanation
Indices: 1871--2037 Score: 110
Period size: 31 Copynumber: 4.7 Consensus size: 34
1861 TACTCTCTCC
*
1871 CTTAAGTATCAATTTACTGATTAATCCCTTGACT
1 CTTAATTATCAATTTACTGATTAATCCCTTGACT
* *
1905 CTTAATTA-CTGATTTACTGATTACTATTTTTACCTTGACT
1 CTTAATTATC-AATTTACTGATTA--A----TCCCTTGACT
*
1945 CTTGATTATCAATTTTACTGATTAATCCC-T---T
1 CTTAATTATCAA-TTTACTGATTAATCCCTTGACT
* * *
1976 CTTAATTATTAATTTTACTGATTACTATTACTTTGACT
1 CTTAATTATCAA-TTTACTGATTA--A-TCCCTTGACT
*
2014 CTTAATTATCGATTTTACTGATTA
1 CTTAATTATC-AATTTACTGATTA
2038 CTTCTTTTGC
Statistics
Matches: 104, Mismatches: 12, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
31 23 0.22
33 2 0.02
34 22 0.21
35 4 0.04
36 1 0.01
38 21 0.20
39 2 0.02
40 17 0.16
41 12 0.12
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.49
Consensus pattern (34 bp):
CTTAATTATCAATTTACTGATTAATCCCTTGACT
Found at i:2029 original size:69 final size:71
Alignment explanation
Indices: 1871--2037 Score: 207
Period size: 69 Copynumber: 2.3 Consensus size: 71
1861 TACTCTCTCC
* *
1871 CTTAAGTATCAA-TTTACTGATTAATCCCTTGACTCTTAATTACTGATTTACTGATTACTATTTT
1 CTTAATTATCAATTTTACTGATTAATCCCTT-A-TCTTAATTACTAATTTACTGATTACTA--TT
1935 TACCTTGACT
62 TACCTTGACT
* *
1945 CTTGATTATCAATTTTACTGATTAATCCC-T-TCTTAATTATTAATTTTACTGATTACTA-TTAC
1 CTTAATTATCAATTTTACTGATTAATCCCTTATCTTAATTACTAA-TTTACTGATTACTATTTAC
*
2007 TTTGACT
65 CTTGACT
*
2014 CTTAATTATCGATTTTACTGATTA
1 CTTAATTATCAATTTTACTGATTA
2038 CTTCTTTTGC
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
69 32 0.38
71 11 0.13
72 14 0.17
74 11 0.13
75 16 0.19
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.49
Consensus pattern (71 bp):
CTTAATTATCAATTTTACTGATTAATCCCTTATCTTAATTACTAATTTACTGATTACTATTTACC
TTGACT
Found at i:2137 original size:36 final size:33
Alignment explanation
Indices: 2070--2252 Score: 160
Period size: 36 Copynumber: 5.5 Consensus size: 33
2060 TTGATTACCA
* * * *
2070 TTTTTCTGATTATTTCTTCTACTTTTGCTCTTTCAC
1 TTTTACTGATTACTTCTTTTACTTTTACTC--TC-C
* *
2106 TTTTACTGATTACTTCTTTTTCGTTTACTCT--
1 TTTTACTGATTACTTCTTTTACTTTTACTCTCC
*
2137 TTTTACTGATTACTTCTTTTGCTTTTA--CTCC
1 TTTTACTGATTACTTCTTTTACTTTTACTCTCC
*
2168 TTTTACTGATTACTTCTTTTACTTTTACTCTTTTAC
1 TTTTACTGATTACTTCTTTTACTTTTACTC---TCC
* * **
2204 TCTTACTGATTACTTATTTTACTTTTACTC-AA
1 TTTTACTGATTACTTCTTTTACTTTTACTCTCC
*
2236 TTCTACTGATTACTTCT
1 TTTTACTGATTACTTCT
2253 CTTGATTACC
Statistics
Matches: 124, Mismatches: 16, Indels: 18
0.78 0.10 0.11
Matches are distributed among these distances:
29 2 0.02
31 51 0.41
32 15 0.12
33 1 0.01
34 1 0.01
36 54 0.44
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (33 bp):
TTTTACTGATTACTTCTTTTACTTTTACTCTCC
Found at i:2144 original size:31 final size:32
Alignment explanation
Indices: 2070--2252 Score: 174
Period size: 31 Copynumber: 5.6 Consensus size: 32
2060 TTGATTACCA
* * *
2070 TTTTT-CTGATTATTTCTTCTACTTTTGCTCTT
1 TTTTTACTGATTACTTCTTTTACTTTTACTC-T
* *
2102 TCACTTTTACTGATTACTTCTTTTTCGTTTACTC-
1 T---TTTTACTGATTACTTCTTTTACTTTTACTCT
*
2136 TTTTTACTGATTACTTCTTTTGCTTTTACTC-
1 TTTTTACTGATTACTTCTTTTACTTTTACTCT
*
2167 CTTTTACTGATTACTTCTTTTACTTTTACTCTT
1 TTTTTACTGATTACTTCTTTTACTTTTACTC-T
* *
2200 TTACTCTTACTGATTACTTATTTTACTTTTACTCA
1 TT--T-TTACTGATTACTTCTTTTACTTTTACTCT
* *
2235 ATTCTACTGATTACTTCT
1 TTTTTACTGATTACTTCT
2253 CTTGATTACC
Statistics
Matches: 127, Mismatches: 15, Indels: 18
0.79 0.09 0.11
Matches are distributed among these distances:
31 57 0.45
32 14 0.11
33 2 0.02
34 1 0.01
35 6 0.05
36 47 0.37
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (32 bp):
TTTTTACTGATTACTTCTTTTACTTTTACTCT
Found at i:2156 original size:16 final size:16
Alignment explanation
Indices: 2105--2204 Score: 102
Period size: 16 Copynumber: 6.5 Consensus size: 16
2095 TGCTCTTTCA
2105 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
* *
2121 CTTTTTC-GTTTAC-T
1 CTTTTACTGATTACTT
2135 CTTTTTACTGATTACTT
1 C-TTTTACTGATTACTT
* * *
2152 CTTTTGCT-TTTACTC
1 CTTTTACTGATTACTT
2167 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
*
2183 CTTTTACT-TTTAC-T
1 CTTTTACTGATTACTT
2197 CTTTTACT
1 CTTTTACT
2205 CTTACTGATT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
14 11 0.16
15 26 0.38
16 30 0.43
17 2 0.03
ACGTcount: A:0.14, C:0.21, G:0.05, T:0.60
Consensus pattern (16 bp):
CTTTTACTGATTACTT
Found at i:2183 original size:62 final size:66
Alignment explanation
Indices: 2102--2252 Score: 202
Period size: 62 Copynumber: 2.3 Consensus size: 66
2092 TTTTGCTCTT
* * *
2102 TCACTTTTACTGATTACTTCTTTTTCGTTTACTC-TT-T-TTACTGATTACTTCTTTTGCTTTTA
1 TCACTTTTACTGATTACTTCTTTTACGTTTACTCTTTATCTTACTGATTACTTATTTTACTTTTA
2164 C
66 C
*
2165 TC-CTTTTACTGATTACTTCTTTTACTTTTACTCTTTTACTCTTACTGATTACTTATTTTACTTT
1 TCACTTTTACTGATTACTTCTTTTACGTTTACTC-TTTA-TCTTACTGATTACTTATTTTACTTT
2229 TAC
64 TAC
* *
2232 TCAATTCTACTGATTACTTCT
1 TCACTTTTACTGATTACTTCT
2253 CTTGATTACC
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
62 29 0.38
63 2 0.03
64 2 0.03
66 1 0.01
67 26 0.34
68 16 0.21
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (66 bp):
TCACTTTTACTGATTACTTCTTTTACGTTTACTCTTTATCTTACTGATTACTTATTTTACTTTTA
C
Found at i:2305 original size:98 final size:95
Alignment explanation
Indices: 2050--2294 Score: 287
Period size: 98 Copynumber: 2.5 Consensus size: 95
2040 TCTTTTGCTA
* * *
2050 ATTACTTCTCTTGATTACCATTTTTCTGATTATTTCTTCTACTTTT-GCTCTTTCACTTTTACTG
1 ATTACTTCTCTTGATTACCATTTTACTGATTATTTCTTTTACTTTTAGCTCTTT-ACTCTTACTG
* * * *
2114 ATTACTTCTTTTTCGTTTACTCTTTTTACTG
65 ATTACTTATTTTACGTTTACTCATTCTACTG
* * * *
2145 ATTACTTCTTTTGCTTTTACTCCTTTTACTGATTACTTCTTTTACTTTTA-CTCTTTTACTCTTA
1 ATTACTTCTCTTG--ATTAC-CATTTTACTGATTATTTCTTTTACTTTTAGCTC-TTTACTCTTA
*
2209 CTGATTACTTATTTTACTTTTACTCAATTCTACTG
62 CTGATTACTTATTTTACGTTTACTC-ATTCTACTG
* *
2244 ATTACTTCTCTTGATTACCAATTTACTGCTTATTTCTTTTACTTTTTAGCT
1 ATTACTTCTCTTGATTACCATTTTACTGATTATTTCTTTTAC-TTTTAGCT
2295 TAATTACTCT
Statistics
Matches: 124, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
95 12 0.10
96 20 0.16
97 13 0.10
98 57 0.46
99 22 0.18
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (95 bp):
ATTACTTCTCTTGATTACCATTTTACTGATTATTTCTTTTACTTTTAGCTCTTTACTCTTACTGA
TTACTTATTTTACGTTTACTCATTCTACTG
Found at i:12831 original size:2 final size:2
Alignment explanation
Indices: 12824--12855 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12814 AGAGATTAAT
12824 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
12856 CACTAGATAA
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:13566 original size:178 final size:178
Alignment explanation
Indices: 13259--13582 Score: 436
Period size: 178 Copynumber: 1.8 Consensus size: 178
13249 CCAATACTTT
*
13259 GGAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTTGAGTCCTTCATGAAAGTTGTAGATC
1 GGAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATC
* * * * * ** *
13324 ATGGAATAACCTTTCAAAAGACATTTGAATCATCTCAATCAGACATCTGGAACAAAAGTTATATA
66 ATGGAATAACCTTTCAAAAGAAACTTAAATCACCTCAATCAGACAACCAGAACAAAAATTATATA
* *
13389 ATATTAAGTGGACCGTCTGTTCTCGTTAATCGAAACAACATATTTTTC
131 ATATTAAATAGACCGTCTGTTCTCGTTAATCGAAACAACATATTTTTC
13437 GGAAGCATTTTTTATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGAT
1 GGAAGCATTTTTTATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGAT
** * * * * * *
13501 CATGGAATAATTTTTTAATAGAAACTTAAATCGCCTTAATCATATAACCAGAA-AGAAAATTATA
65 CATGGAATAACCTTTCAAAAGAAACTTAAATCACCTCAATCAGACAACCAGAACA-AAAATTATA
*
13565 TAATGTTAAATAGACCGT
129 TAATATTAAATAGACCGT
13583 TTAGACAAAT
Statistics
Matches: 124, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
177 5 0.04
178 119 0.96
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (178 bp):
GGAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATC
ATGGAATAACCTTTCAAAAGAAACTTAAATCACCTCAATCAGACAACCAGAACAAAAATTATATA
ATATTAAATAGACCGTCTGTTCTCGTTAATCGAAACAACATATTTTTC
Found at i:13817 original size:21 final size:21
Alignment explanation
Indices: 13793--13832 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13783 ATATTTATAT
*
13793 GTTATATATATATATATATTG
1 GTTAAATATATATATATATTG
13814 GTTAAATATATATATATAT
1 GTTAAATATATATATATAT
13833 ATATATGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
GTTAAATATATATATATATTG
Found at i:20997 original size:40 final size:40
Alignment explanation
Indices: 20950--21031 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
20940 TGCTCTACTT
*
20950 CTTTATAATTTTGTAAAATGTTTGCCAAGTTGATTGACAA
1 CTTTATAAATTTGTAAAATGTTTGCCAAGTTGATTGACAA
20990 CTTTATAAATTTGTAAAATGTTTGCCAAGTTGATTGACAA
1 CTTTATAAATTTGTAAAATGTTTGCCAAGTTGATTGACAA
21030 CT
1 CT
21032 CTTTTGGCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (40 bp):
CTTTATAAATTTGTAAAATGTTTGCCAAGTTGATTGACAA
Done.