Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012265.1 Corchorus capsularis cultivar CVL-1 contig12286, 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: 26332
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4404 original size:14 final size:14
Alignment explanation
Indices: 4385--4413 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4375 CCCATTTCAT
4385 TACCATTTCCAAAA
1 TACCATTTCCAAAA
4399 TACCATTTCCAAAA
1 TACCATTTCCAAAA
4413 T
1 T
4414 GCAAAGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (14 bp):
TACCATTTCCAAAA
Found at i:6303 original size:14 final size:14
Alignment explanation
Indices: 6284--6319 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
6274 TACAGAAACT
*
6284 AAAAAAATATATAC
1 AAAAAAATACATAC
6298 AAAAAAATACATAC
1 AAAAAAATACATAC
6312 AGAAAAAA
1 A-AAAAAA
6320 GAAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAAAAATACATAC
Found at i:7644 original size:27 final size:26
Alignment explanation
Indices: 7606--7744 Score: 140
Period size: 26 Copynumber: 5.3 Consensus size: 26
7596 GTAATTAGTA
7606 ATCAGTAAAAAGAGTAAGAAAAGAGCC
1 ATCAGTAAAAAGAGTAAGAAAAGAG-C
* * *
7633 ATCAGTAAAAAGAGTAAG-GAACAGT
1 ATCAGTAAAAAGAGTAAGAAAAGAGC
*
7658 ATTCAGTAAAAAGAATAAGAAAAGAGTC
1 A-TCAGTAAAAAGAGTAAGAAAAGAG-C
* *
7686 ATCAGTAAAAAGAGTAGGAAATA-A-T
1 ATCAGTAAAAAGAGTAAGAAA-AGAGC
*
7711 ATTCAGTAAAAAGAGTAAGAAAAGCGC
1 A-TCAGTAAAAAGAGTAAGAAAAGAGC
*
7738 ATTAGTA
1 ATCAGTA
7745 GTCAACAAAG
Statistics
Matches: 91, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
25 3 0.03
26 44 0.48
27 42 0.46
28 2 0.02
ACGTcount: A:0.54, C:0.08, G:0.21, T:0.17
Consensus pattern (26 bp):
ATCAGTAAAAAGAGTAAGAAAAGAGC
Found at i:7663 original size:26 final size:26
Alignment explanation
Indices: 7606--7734 Score: 147
Period size: 27 Copynumber: 4.9 Consensus size: 26
7596 GTAATTAGTA
*
7606 ATCAGTAAAAAGAGTAAGAAAAGAGCC
1 ATCAGTAAAAAGAGTAAGAAAAGAG-T
* *
7633 ATCAGTAAAAAGAGTAAG-GAACAGT
1 ATCAGTAAAAAGAGTAAGAAAAGAGT
*
7658 ATTCAGTAAAAAGAATAAGAAAAGAGT
1 A-TCAGTAAAAAGAGTAAGAAAAGAGT
*
7685 CATCAGTAAAAAGAGTAGGAAATA-A-T
1 -ATCAGTAAAAAGAGTAAGAAA-AGAGT
7711 ATTCAGTAAAAAGAGTAAGAAAAG
1 A-TCAGTAAAAAGAGTAAGAAAAG
7735 CGCATTAGTA
Statistics
Matches: 87, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.03
26 40 0.46
27 42 0.48
28 2 0.02
ACGTcount: A:0.56, C:0.07, G:0.21, T:0.16
Consensus pattern (26 bp):
ATCAGTAAAAAGAGTAAGAAAAGAGT
Found at i:7665 original size:53 final size:53
Alignment explanation
Indices: 7602--7734 Score: 205
Period size: 53 Copynumber: 2.5 Consensus size: 53
7592 ATTAGTAATT
*
7602 AGTAATCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAAGG-AAC
1 AGTATTCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGT-AGGAAAC
* * *
7655 AGTATTCAGTAAAAAGAATAAGAAAAGAGTCATCAGTAAAAAGAGTAGGAAAT
1 AGTATTCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAGGAAAC
*
7708 AATATTCAGTAAAAAGAGTAAGAAAAG
1 AGTATTCAGTAAAAAGAGTAAGAAAAG
7735 CGCATTAGTA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
52 3 0.04
53 70 0.96
ACGTcount: A:0.56, C:0.07, G:0.21, T:0.17
Consensus pattern (53 bp):
AGTATTCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAGGAAAC
Found at i:7849 original size:35 final size:35
Alignment explanation
Indices: 7808--8096 Score: 179
Period size: 35 Copynumber: 8.1 Consensus size: 35
7798 TTGAAAAGGC
* *
7808 AATCAGTAAAGAGTAAAATGGTAAAAAGTAATG-GT
1 AATCAGTAAAGAG-AAAATGGTAAAGAGTAAAGAGT
* * *
7843 AATCAGTAAACA-ATGAAATAGTAAAGAGTAAAAAGT
1 AATCAGTAAAGAGA--AAATGGTAAAGAGTAAAGAGT
*
7879 AATCAGTAAAGAG-AAATGGTAAGGAGTAATAGAGT
1 AATCAGTAAAGAGAAAATGGTAAAGAGTAA-AGAGT
*
7914 AATCAGTGGAA-A-AAAATGGTAAAGAGTAAAGAGT
1 AATCAGT-AAAGAGAAAATGGTAAAGAGTAAAGAGT
* *
7948 -A-CAGTAAAG-GAAAAATGGTAAAGAATGAAGAGT
1 AATCAGTAAAGAG-AAAATGGTAAAGAGTAAAGAGT
* * * *
7981 AATTAGCGAAATGGTAGAGTAATAGT-AA-AGTAAAGAG-
1 AATCAG-TAAA--G-AGA-AAATGGTAAAGAGTAAAGAGT
* *
8018 AGATCAGTAAAAAGAAAATAGTAAAGAGTAAAGTAAAAAGT
1 A-ATCAGTAAAGAGAAAATGGTAAAGAGTAAAG-----AGT
**
8059 AATCAGTAAAGA-AAATATGGTAATCAGTAAAGAGT
1 AATCAGTAAAGAGAAA-ATGGTAAAGAGTAAAGAGT
8094 AAT
1 AAT
8097 AGTGATCAGT
Statistics
Matches: 198, Mismatches: 28, Indels: 56
0.70 0.10 0.20
Matches are distributed among these distances:
31 2 0.01
32 4 0.02
33 28 0.14
34 25 0.13
35 67 0.34
36 18 0.09
37 4 0.02
38 12 0.06
39 6 0.03
40 31 0.16
41 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (35 bp):
AATCAGTAAAGAGAAAATGGTAAAGAGTAAAGAGT
Found at i:7888 original size:21 final size:20
Alignment explanation
Indices: 7828--7891 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 20
7818 GAGTAAAATG
* **
7828 GTAAAAAGTAATGGTAATCA
1 GTAAAAAGTAATAGTAAAGA
*
7848 GTAAACAATGAAATAGTAAAGA
1 GTAAA-AA-GTAATAGTAAAGA
7870 GTAAAAAGTAATCAGTAAAGA
1 GTAAAAAGTAAT-AGTAAAGA
7891 G
1 G
7892 AAATGGTAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 9 0.25
21 13 0.36
22 14 0.39
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (20 bp):
GTAAAAAGTAATAGTAAAGA
Found at i:8059 original size:19 final size:19
Alignment explanation
Indices: 8028--8091 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
8018 AGATCAGTAA
*
8028 AAAGAAAATAGTAAAGAGT
1 AAAGAAAATAGTAAACAGT
*
8047 AAAGTAAAA-AGTAATCAGT
1 AAAG-AAAATAGTAAACAGT
*
8066 AAAGAAAATATGGTAATCAGT
1 AAAGAAAATA--GTAAACAGT
8087 AAAGA
1 AAAGA
8092 GTAATAGTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.10
19 17 0.44
20 4 0.10
21 14 0.36
ACGTcount: A:0.59, C:0.03, G:0.19, T:0.19
Consensus pattern (19 bp):
AAAGAAAATAGTAAACAGT
Found at i:8160 original size:22 final size:22
Alignment explanation
Indices: 8047--8286 Score: 184
Period size: 20 Copynumber: 11.4 Consensus size: 22
8037 AGTAAAGAGT
8047 AAAGTAAAAA-GTAATCAGT--
1 AAAGTAAAAAGGTAATCAGTAA
8066 AAAG-AAAATATGGTAATCAGTAA
1 AAAGTAAAA-A-GGTAATCAGTAA
* * *
8089 AGAGT-AATA-GTGATCAGTAA
1 AAAGTAAAAAGGTAATCAGTAA
* * * *
8109 GAAGT--AATGGCAATCAATAA
1 AAAGTAAAAAGGTAATCAGTAA
* *
8129 AAAGTAAAAAAGGTAATTAATAA
1 AAAGT-AAAAAGGTAATCAGTAA
*
8152 AAAGTAAAATGGTAATCAGTAA
1 AAAGTAAAAAGGTAATCAGTAA
*
8174 AAAGT--AAAGGTAATCAGTGA
1 AAAGTAAAAAGGTAATCAGTAA
* * *
8194 AATGTAAAATGGTAATTAG-AA
1 AAAGTAAAAAGGTAATCAGTAA
8215 AAGAGT--AAAGGTAATCAGTAA
1 AA-AGTAAAAAGGTAATCAGTAA
* *
8236 AAAGTAAAATGGTAATTAGTAA
1 AAAGTAAAAAGGTAATCAGTAA
*
8258 AAAGTAAAGA-GTAATCAGTAA
1 AAAGTAAAAAGGTAATCAGTAA
*
8279 AGAGTAAA
1 AAAGTAAA
8287 GAGTGAAAAG
Statistics
Matches: 173, Mismatches: 32, Indels: 30
0.74 0.14 0.13
Matches are distributed among these distances:
18 4 0.02
19 6 0.03
20 55 0.32
21 33 0.19
22 53 0.31
23 22 0.13
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.22
Consensus pattern (22 bp):
AAAGTAAAAAGGTAATCAGTAA
Found at i:8187 original size:20 final size:20
Alignment explanation
Indices: 8047--8287 Score: 184
Period size: 21 Copynumber: 11.4 Consensus size: 20
8037 AGTAAAGAGT
*
8047 AAAGTAAAAAGTAATCAGTAA
1 AAAGT-AAAGGTAATCAGTAA
8068 AGAA--AATATGGTAATCAGTAA
1 A-AAGTAA-A-GGTAATCAGTAA
* *
8089 AGAGTAATA-GTGATCAGTAA
1 AAAGTAA-AGGTAATCAGTAA
* * * *
8109 GAAGTAATGGCAATCAATAA
1 AAAGTAAAGGTAATCAGTAA
* *
8129 AAAGTAAAAAAGGTAATTAATAA
1 AAAGT---AAAGGTAATCAGTAA
8152 AAAGTAAAATGGTAATCAGTAA
1 AAAGT-AAA-GGTAATCAGTAA
*
8174 AAAGTAAAGGTAATCAGTGA
1 AAAGTAAAGGTAATCAGTAA
* *
8194 AATGTAAAATGGTAATTAG-AA
1 AAAGT-AAA-GGTAATCAGTAA
8215 AAGAGTAAAGGTAATCAGTAA
1 AA-AGTAAAGGTAATCAGTAA
*
8236 AAAGTAAAATGGTAATTAGTAA
1 AAAGT-AAA-GGTAATCAGTAA
8258 AAAGTAAAGAGTAATCAGTAA
1 AAAGTAAAG-GTAATCAGTAA
*
8279 AGAGTAAAG
1 AAAGTAAAG
8288 AGTGAAAAGT
Statistics
Matches: 179, Mismatches: 24, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.01
20 56 0.31
21 57 0.32
22 47 0.26
23 17 0.09
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAGTAAAGGTAATCAGTAA
Found at i:8201 original size:42 final size:41
Alignment explanation
Indices: 8047--8286 Score: 229
Period size: 42 Copynumber: 5.7 Consensus size: 41
8037 AGTAAAGAGT
* *
8047 AAAGTAAAAAGTAATCAGT-AAAGAAAATATGGTAATCAGTAA
1 AAAGT-AAAGGTAATCAGTAAAAGTAAA-ATGGTAATCAGTAA
* * * *
8089 AGAGTAATA-GTGATCAGTAAGAAGT--AATGGCAATCAATAA
1 AAAGTAA-AGGTAATCAGTAA-AAGTAAAATGGTAATCAGTAA
* *
8129 AAAGTAAAAAAGGTAATTAATAAAAAGTAAAATGGTAATCAGTAA
1 AAAGT---AAAGGTAATCAGT-AAAAGTAAAATGGTAATCAGTAA
* *
8174 AAAGTAAAGGTAATCAGTGAAATGTAAAATGGTAATTAG-AA
1 AAAGTAAAGGTAATCAGT-AAAAGTAAAATGGTAATCAGTAA
*
8215 AAGAGTAAAGGTAATCAGTAAAAAGTAAAATGGTAATTAGTAA
1 AA-AGTAAAGGTAATCAGT-AAAAGTAAAATGGTAATCAGTAA
8258 AAAGTAAAGAGTAATCAGTAAAGAGTAAA
1 AAAGTAAAG-GTAATCAGTAAA-AGTAAA
8287 GAGTGAAAAG
Statistics
Matches: 166, Mismatches: 18, Indels: 27
0.79 0.09 0.13
Matches are distributed among these distances:
40 16 0.10
41 15 0.09
42 81 0.49
43 34 0.20
44 2 0.01
45 18 0.11
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.22
Consensus pattern (41 bp):
AAAGTAAAGGTAATCAGTAAAAGTAAAATGGTAATCAGTAA
Found at i:8270 original size:14 final size:14
Alignment explanation
Indices: 8213--8309 Score: 54
Period size: 14 Copynumber: 6.9 Consensus size: 14
8203 TGGTAATTAG
8213 AAAAGAGTAAAG-GT
1 AAAA-AGTAAAGAGT
** *
8227 AATCAGTAAAAAGT
1 AAAAAGTAAAGAGT
* **
8241 AAAATGGTAATTAGT
1 AAAA-AGTAAAGAGT
8256 AAAAAGTAAAGAGT
1 AAAAAGTAAAGAGT
**
8270 AATCAGTAAAGAGT
1 AAAAAGTAAAGAGT
*
8284 AAAGAGTGAAA-AGT
1 AAAAAGT-AAAGAGT
**
8298 AATCAGTAAAGA
1 AAAAAGTAAAGA
8310 AAAAATAGTA
Statistics
Matches: 62, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
13 9 0.15
14 39 0.63
15 14 0.23
ACGTcount: A:0.56, C:0.03, G:0.22, T:0.20
Consensus pattern (14 bp):
AAAAAGTAAAGAGT
Found at i:8378 original size:27 final size:29
Alignment explanation
Indices: 8333--8390 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
8323 AGTGAGAAGA
*
8333 AATCAGTAAAATGGTAAATGATAAAGAGT
1 AATCAGTAAAATGGAAAATGATAAAGAGT
* *
8362 AATCAGT-AAA-GGAAAATGGTAGAGAGT
1 AATCAGTAAAATGGAAAATGATAAAGAGT
8389 AA
1 AA
8391 AATATTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 16 0.62
28 3 0.12
29 7 0.27
ACGTcount: A:0.52, C:0.03, G:0.24, T:0.21
Consensus pattern (29 bp):
AATCAGTAAAATGGAAAATGATAAAGAGT
Found at i:8405 original size:42 final size:43
Alignment explanation
Indices: 8366--8490 Score: 157
Period size: 42 Copynumber: 3.0 Consensus size: 43
8356 AAGAGTAATC
* *
8366 AGTAAAGGAAAAT-GGTAGAGAGTAAAATATTAATCAGTAAAA
1 AGTAAAGGAAAATCAGTAAAGAGTAAAATATTAATCAGTAAAA
* * *
8408 AGTAAAGG-CAATCAGTAAAGAATAAAATATTAATCAGTAAAG
1 AGTAAAGGAAAATCAGTAAAGAGTAAAATATTAATCAGTAAAA
* *
8450 AGTAAA-GAGTAATCAGTAAAGAGTAAAATAGTAATCAGTAA
1 AGTAAAGGA-AAATCAGTAAAGAGTAAAATATTAATCAGTAA
8491 GTGGTAATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.06
42 39 0.54
43 29 0.40
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (43 bp):
AGTAAAGGAAAATCAGTAAAGAGTAAAATATTAATCAGTAAAA
Found at i:8445 original size:22 final size:22
Alignment explanation
Indices: 8388--8490 Score: 106
Period size: 22 Copynumber: 4.8 Consensus size: 22
8378 TGGTAGAGAG
*
8388 TAAAATATTAATCAGTAAA-AA
1 TAAAATAGTAATCAGTAAAGAA
* *
8409 GT-AAA-GGCAATCAGTAAAGAA
1 -TAAAATAGTAATCAGTAAAGAA
* *
8430 TAAAATATTAATCAGTAAAGAG
1 TAAAATAGTAATCAGTAAAGAA
* *
8452 T-AAAGAGTAATCAGTAAAGAG
1 TAAAATAGTAATCAGTAAAGAA
8473 TAAAATAGTAATCAGTAA
1 TAAAATAGTAATCAGTAA
8491 GTGGTAATTA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.16
21 27 0.40
22 29 0.43
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.23
Consensus pattern (22 bp):
TAAAATAGTAATCAGTAAAGAA
Found at i:8455 original size:7 final size:7
Alignment explanation
Indices: 8443--8476 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
8433 AATATTAATC
8443 AGTAAAG
1 AGTAAAG
8450 AGTAAAG
1 AGTAAAG
**
8457 AGTAATC
1 AGTAAAG
8464 AGTAAAG
1 AGTAAAG
8471 AGTAAA
1 AGTAAA
8477 ATAGTAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.18
Consensus pattern (7 bp):
AGTAAAG
Found at i:8478 original size:43 final size:42
Alignment explanation
Indices: 8384--8490 Score: 169
Period size: 43 Copynumber: 2.5 Consensus size: 42
8374 AAAATGGTAG
8384 AGAGTAAAATATTAATCAGTAAAAAGTAAAGGCAATCAGTAA
1 AGAGTAAAATATTAATCAGTAAAAAGTAAAGGCAATCAGTAA
* * *
8426 AGAATAAAATATTAATCAGTAAAGAGTAAAGAGTAATCAGTAA
1 AGAGTAAAATATTAATCAGTAAAAAGTAAAG-GCAATCAGTAA
*
8469 AGAGTAAAATAGTAATCAGTAA
1 AGAGTAAAATATTAATCAGTAA
8491 GTGGTAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
42 29 0.49
43 30 0.51
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.22
Consensus pattern (42 bp):
AGAGTAAAATATTAATCAGTAAAAAGTAAAGGCAATCAGTAA
Found at i:9337 original size:20 final size:21
Alignment explanation
Indices: 9298--9337 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9288 GCTTGGTCCC
* *
9298 TTTGCTTCCAAATTTCAATTT
1 TTTGCTACCAAATCTCAATTT
9319 TTTGCTACCAAA-CTCAATT
1 TTTGCTACCAAATCTCAATT
9338 CCAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTGCTACCAAATCTCAATTT
Found at i:11495 original size:20 final size:20
Alignment explanation
Indices: 11470--11514 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
11460 AAGAATTGTA
11470 GCTTCTTGGAAATGGCTCTT
1 GCTTCTTGGAAATGGCTCTT
11490 GCTTCTTGGAAATGGCTCTT
1 GCTTCTTGGAAATGGCTCTT
11510 GCTTC
1 GCTTC
11515 CTTTGAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
GCTTCTTGGAAATGGCTCTT
Found at i:11529 original size:21 final size:21
Alignment explanation
Indices: 11470--11538 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 21
11460 AAGAATTGTA
**
11470 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
**
11490 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
11510 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
11531 GCATTCCT
1 GC-TTCCT
11539 AAAACATTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 24 0.55
21 15 0.34
22 5 0.11
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:20047 original size:30 final size:31
Alignment explanation
Indices: 20013--20095 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 31
20003 TTCTCGTCAC
*
20013 CCAAAATAGATTTATTTTCAATGC-CATCAA
1 CCAAAACAGATTTATTTTCAATGCTCATCAA
* *
20043 CCAAAACAGGA-TTATTTGCAATGCTATGATCAA
1 CCAAAACA-GATTTATTTTCAATGC--TCATCAA
*
20076 CCAAAACAGATTTGTTTTCA
1 CCAAAACAGATTTATTTTCA
20096 TCATCCAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
30 19 0.44
31 2 0.05
32 2 0.05
33 20 0.47
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (31 bp):
CCAAAACAGATTTATTTTCAATGCTCATCAA
Found at i:20120 original size:24 final size:24
Alignment explanation
Indices: 20071--20122 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
20061 CAATGCTATG
*
20071 ATCAACCAAAACAGATTTGTTTTC
1 ATCAACCAAAACAGATTTGTTATC
*
20095 ATCATCCAAAACAGATTTAG-TATC
1 ATCAACCAAAACAGATTT-GTTATC
20119 ATCA
1 ATCA
20123 CAAACAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (24 bp):
ATCAACCAAAACAGATTTGTTATC
Found at i:20144 original size:33 final size:33
Alignment explanation
Indices: 20101--20194 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
20091 TTTCATCATC
*
20101 CAAAACAGATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* * *
20134 TAAAACAGATTTAGTGTCATTGCAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
** *
20167 CAAATTAGGTTTAGTATCATCGCAAACA
1 CAAAACAGATTTAGTATCATCGCAAACA
20195 TCATCTAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.26
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:21723 original size:8 final size:8
Alignment explanation
Indices: 21695--21728 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
21685 GAATCGGCTA
21695 TGAATTTT
1 TGAATTTT
*
21703 TGAAGTTTC
1 TGAA-TTTT
21712 TGAATTTT
1 TGAATTTT
21720 TGAATTTT
1 TGAATTTT
21728 T
1 T
21729 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:24684 original size:35 final size:34
Alignment explanation
Indices: 24638--24711 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 34
24628 GTGAATGGAA
*
24638 GTTTTTTTTTTTTT-AAGTATAATAGAGGTATATTC
1 GTTTTTTTTTTTTTGCA-TA-AATAGAGGTATATTC
*
24673 GTTTTTTTTTTTTTGCATCAAATAGATGTATATTC
1 GTTTTTTTTTTTTTGCAT-AAATAGAGGTATATTC
24708 GTTT
1 GTTT
24712 ATTAGTCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 33 0.94
36 2 0.06
ACGTcount: A:0.23, C:0.05, G:0.14, T:0.58
Consensus pattern (34 bp):
GTTTTTTTTTTTTTGCATAAATAGAGGTATATTC
Done.