Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015896.1 Corchorus capsularis cultivar CVL-1 contig15917, 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: 55186
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:3598 original size:19 final size:18
Alignment explanation
Indices: 3574--3609 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3564 TGAAGATTTC
3574 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
3593 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
3610 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:6502 original size:26 final size:26
Alignment explanation
Indices: 6473--6524 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6463 AACATTAAAG
6473 GAAACAAGGAACATGCAAGGGGCTGT
1 GAAACAAGGAACATGCAAGGGGCTGT
6499 GAAACAAGGAACATGCAAGGGGCTGT
1 GAAACAAGGAACATGCAAGGGGCTGT
6525 CAAGCAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.35, T:0.12
Consensus pattern (26 bp):
GAAACAAGGAACATGCAAGGGGCTGT
Found at i:6532 original size:26 final size:26
Alignment explanation
Indices: 6474--6532 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
6464 ACATTAAAGG
*
6474 AAACAAGGAACATGCAAGGGGCTGTG
1 AAACAAGGAACATGCAAGGGGCTGTC
6500 AAACAAGGAACATGCAAGGGGCTGTC
1 AAACAAGGAACATGCAAGGGGCTGTC
*
6526 AAGCAAG
1 AAACAAG
6533 CATGCACCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.32, T:0.10
Consensus pattern (26 bp):
AAACAAGGAACATGCAAGGGGCTGTC
Found at i:9926 original size:27 final size:27
Alignment explanation
Indices: 9888--10013 Score: 154
Period size: 26 Copynumber: 4.7 Consensus size: 27
9878 ATCAGTAATT
9888 AGTAAAAAGAGTAAGAAAAGAGTCA-TC
1 AGTAAAAAGAGTAAGAAAAGAGT-ATTC
* *
9915 AGTAAAAAGAGTAAG-GAACAGTATTC
1 AGTAAAAAGAGTAAGAAAAGAGTATTC
*
9941 AGTAAAAAGAATAAGAAAAGAGTCA-TC
1 AGTAAAAAGAGTAAGAAAAGAGT-ATTC
*
9968 AGTAAAAAGAGTAGGAAATA-A-TATTC
1 AGTAAAAAGAGTAAGAAA-AGAGTATTC
9994 AGTAAAAAGAGTAAGAAAAG
1 AGTAAAAAGAGTAAGAAAAG
10014 CGCGATAGTA
Statistics
Matches: 85, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.04
26 41 0.48
27 39 0.46
28 2 0.02
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.17
Consensus pattern (27 bp):
AGTAAAAAGAGTAAGAAAAGAGTATTC
Found at i:9942 original size:26 final size:28
Alignment explanation
Indices: 9880--10012 Score: 147
Period size: 27 Copynumber: 5.0 Consensus size: 28
9870 AATTAGTAAT
*
9880 CAGTAATT-AGTAAAAAGAGTAAGAAAA
1 CAGTCATTCAGTAAAAAGAGTAAGAAAA
* *
9907 GAGTCA-TCAGTAAAAAGAGTAAG-GAA
1 CAGTCATTCAGTAAAAAGAGTAAGAAAA
*
9933 CAGT-ATTCAGTAAAAAGAATAAGAAAA
1 CAGTCATTCAGTAAAAAGAGTAAGAAAA
* *
9960 GAGTCA-TCAGTAAAAAGAGTAGGAAATA
1 CAGTCATTCAGTAAAAAGAGTAAGAAA-A
9988 -A-T-ATTCAGTAAAAAGAGTAAGAAAA
1 CAGTCATTCAGTAAAAAGAGTAAGAAAA
10013 GCGCGATAGT
Statistics
Matches: 90, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
25 3 0.03
26 42 0.47
27 43 0.48
28 2 0.02
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (28 bp):
CAGTCATTCAGTAAAAAGAGTAAGAAAA
Found at i:9945 original size:53 final size:53
Alignment explanation
Indices: 9880--10013 Score: 209
Period size: 53 Copynumber: 2.5 Consensus size: 53
9870 AATTAGTAAT
9880 CAGTAATT-AGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAAGG-AA
1 CAGT-ATTCAGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGT-AGGAAA
*
9933 CAGTATTCAGTAAAAAGAATAAGAAAAGAGTCATCAGTAAAAAGAGTAGGAAA
1 CAGTATTCAGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAGGAAA
* *
9986 TAATATTCAGTAAAAAGAGTAAGAAAAG
1 CAGTATTCAGTAAAAAGAGTAAGAAAAG
10014 CGCGATAGTA
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
52 6 0.08
53 69 0.92
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (53 bp):
CAGTATTCAGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAGTAGGAAA
Found at i:10243 original size:35 final size:34
Alignment explanation
Indices: 10143--10256 Score: 131
Period size: 35 Copynumber: 3.3 Consensus size: 34
10133 AATAAAATAG
* * * * * *
10143 TAAAAAGTAATAAATAAAGAGAAATGGTAAGGAG
1 TAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAA
*
10177 TAATAGAGTAATCAGTGAA-AAAAATGGTAAAGAA
1 TAA-AGAGTAATCAGTAAAGAAAAATGGTAAAGAA
10211 TAAAGAGTAATCAGTAAAAGAAAAATGGTAAAGAA
1 TAAAGAGTAATCAGT-AAAGAAAAATGGTAAAGAA
*
10246 TGAAGAGTAAT
1 TAAAGAGTAAT
10257 TAGCAAAATG
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
33 12 0.18
34 20 0.29
35 36 0.53
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.19
Consensus pattern (34 bp):
TAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAA
Found at i:10324 original size:35 final size:34
Alignment explanation
Indices: 10087--10256 Score: 122
Period size: 35 Copynumber: 5.1 Consensus size: 34
10077 TTCAAAAGGC
* *
10087 AATCAGTAAAGAGTAAAATGGTAAAAAGTAATG-GT
1 AATCAGTAAA-AG-AAAATGGTAAAGAGTAAAGAGT
* * * *
10122 AATCAGT--AA-ACAAT--AAAATAGTAAAAAGT
1 AATCAGTAAAAGAAAATGGTAAAGAGTAAAGAGT
* * *
10151 AATAAAT-AAAGAGAAATGGTAAGGAGTAATAGAGT
1 AATCAGTAAAAGA-AAATGGTAAAGAGTAA-AGAGT
* *
10186 AATCAGTGAAA-AAAATGGTAAAGAATAAAGAGT
1 AATCAGTAAAAGAAAATGGTAAAGAGTAAAGAGT
* *
10219 AATCAGTAAAAGAAAAATGGTAAAGAATGAAGAGT
1 AATCAGTAAAAG-AAAATGGTAAAGAGTAAAGAGT
10254 AAT
1 AAT
10257 TAGCAAAATG
Statistics
Matches: 107, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
28 8 0.07
29 7 0.07
30 6 0.06
31 1 0.01
32 4 0.04
33 16 0.15
34 21 0.20
35 41 0.38
36 3 0.03
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.20
Consensus pattern (34 bp):
AATCAGTAAAAGAAAATGGTAAAGAGTAAAGAGT
Found at i:10380 original size:20 final size:20
Alignment explanation
Indices: 10354--10409 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
10344 AAAATATGGT
*
10354 AATCAGTAAAGAGTAATAGT
1 AATCAGTAAAGAGTAATAGC
* *
10374 GATCAGT-AAGAAGTAATGGC
1 AATCAGTAAAG-AGTAATAGC
*
10394 AATCAGTAAAAAGTAA
1 AATCAGTAAAGAGTAA
10410 AAAGGTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.10
20 24 0.83
21 2 0.07
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (20 bp):
AATCAGTAAAGAGTAATAGC
Found at i:10427 original size:22 final size:22
Alignment explanation
Indices: 10294--10572 Score: 202
Period size: 22 Copynumber: 13.4 Consensus size: 22
10284 GTAAAGAGAG
*
10294 ATCAGTAAAAAG-AAAATGGTA
1 ATCAGTAAAAAGTAAAAAGGTA
**
10315 AAGAGT--AAAGTAAAAA-GTA
1 ATCAGTAAAAAGTAAAAAGGTA
10334 ATCAGT--AAAG-AAAATATGGTA
1 ATCAGTAAAAAGTAAAA-A-GGTA
* * *
10355 ATCAGTAAAGAGT-AATA-GTG
1 ATCAGTAAAAAGTAAAAAGGTA
* * *
10375 ATCAGTAAGAAGT--AATGGCA
1 ATCAGTAAAAAGTAAAAAGGTA
10395 ATCAGTAAAAAGTAAAAAGGTA
1 ATCAGTAAAAAGTAAAAAGGTA
* * *
10417 ATTAATAAAAAGTAAAATGGTA
1 ATCAGTAAAAAGTAAAAAGGTA
10439 ATCAGTAAAAAGT--AAAGGTA
1 ATCAGTAAAAAGTAAAAAGGTA
* *
10459 ATCAGTGAAAAGTAAAATGGTA
1 ATCAGTAAAAAGTAAAAAGGTA
*
10481 AT---TAAAAAG-AGTAAAGGTA
1 ATCAGTAAAAAGTA-AAAAGGTA
*
10500 ATCAGTAAAAAGTAAAATGGTA
1 ATCAGTAAAAAGTAAAAAGGTA
* *
10522 ATTAGTAAAAAGTAAAGAAAG--
1 ATCAGTAAAAAGTAAA-AAGGTA
* *
10543 ATCAGTAAAGAGTGAAAA-GTA
1 ATCAGTAAAAAGTAAAAAGGTA
10564 ATCAGTAAA
1 ATCAGTAAA
10573 GAAAAAATAG
Statistics
Matches: 202, Mismatches: 36, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
18 5 0.02
19 32 0.16
20 50 0.25
21 35 0.17
22 72 0.36
23 8 0.04
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (22 bp):
ATCAGTAAAAAGTAAAAAGGTA
Found at i:10511 original size:41 final size:41
Alignment explanation
Indices: 10281--10538 Score: 212
Period size: 42 Copynumber: 6.2 Consensus size: 41
10271 AGTAAAGAGT
*
10281 AAAGTAAAGAG-AGATCAGTAAAAAG-AAAATGGTAA--AGAGT
1 AAAGTAAAG-GTA-ATCAGTAAAAAGTAAAATGGTAATTAGA-A
* * *
10321 AAAGTAAAAAGTAATCAGTAAAGAA--AATATGGTAATCAGTAA
1 AAAGT-AAAGGTAATCAGTAAA-AAGTAAAATGGTAATTAG-AA
* * * * *
10363 AGAGTAATA-GTGATCAGTAAGAAGT--AATGGCAATCAGTAA
1 AAAGTAA-AGGTAATCAGTAAAAAGTAAAATGGTAATTAG-AA
* * *
10403 AAAGTAAAAAGGTAATTAATAAAAAGTAAAATGGTAATCAGTAA
1 AAAGT--AAAGGTAATCAGTAAAAAGTAAAATGGTAATTAG-AA
*
10447 AAAGTAAAGGTAATCAGTGAAAAGTAAAATGGTAATTA-AA
1 AAAGTAAAGGTAATCAGTAAAAAGTAAAATGGTAATTAGAA
10487 AAGAGTAAAGGTAATCAGTAAAAAGTAAAATGGTAATTAGTAA
1 AA-AGTAAAGGTAATCAGTAAAAAGTAAAATGGTAATTAG-AA
10530 AAAGTAAAG
1 AAAGTAAAG
10539 AAAGATCAGT
Statistics
Matches: 182, Mismatches: 19, Indels: 32
0.78 0.08 0.14
Matches are distributed among these distances:
40 47 0.26
41 54 0.30
42 57 0.31
43 5 0.03
44 19 0.10
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (41 bp):
AAAGTAAAGGTAATCAGTAAAAAGTAAAATGGTAATTAGAA
Found at i:10565 original size:83 final size:82
Alignment explanation
Indices: 10410--10565 Score: 217
Period size: 83 Copynumber: 1.9 Consensus size: 82
10400 TAAAAAGTAA
* **
10410 AAAGGTAATTAATAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAGGTAATCAGTGAAAAGTAAA
1 AAAGGTAATCAATAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAGAAAATCAGTGAAAAGTAAA
10475 ATGGTAATTAAAAAGAGT
66 A-GGTAATTAAAAAGAGT
* *
10493 AAAGGTAATCAGTAAAAAGTAAAATGGTAATTAGTAAAAAGTAAAGAAAGATCAGT-AAAGAGTG
1 AAAGGTAATCAATAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAGAAA-ATCAGTGAAA-AGT-
10557 AAAA-GTAAT
63 AAAAGGTAAT
10566 CAGTAAAGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
83 52 0.80
84 9 0.14
85 4 0.06
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.22
Consensus pattern (82 bp):
AAAGGTAATCAATAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAGAAAATCAGTGAAAAGTAAA
AGGTAATTAAAAAGAGT
Found at i:10585 original size:35 final size:35
Alignment explanation
Indices: 10532--10607 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
10522 ATTAGTAAAA
* *
10532 AGTAAAGAAAGATCAGTAA-AGAGTGAAAAGTAATC
1 AGTAAAGAAAAATCAGTAAGA-AGTGAAAAGAAATC
*
10567 AGTAAAGAAAAAAT-AGTAAGAAGTGAGAAGAAATC
1 AGTAAAG-AAAAATCAGTAAGAAGTGAAAAGAAATC
10602 AGTAAA
1 AGTAAA
10608 ATGGTAAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 30 0.83
36 6 0.17
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.16
Consensus pattern (35 bp):
AGTAAAGAAAAATCAGTAAGAAGTGAAAAGAAATC
Found at i:10647 original size:27 final size:29
Alignment explanation
Indices: 10598--10655 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
10588 AGTGAGAAGA
*
10598 AATCAGTAAAATGGTAAAGGATAAAGAGT
1 AATCAGTAAAATGGAAAAGGATAAAGAGT
* *
10627 AATCAGT-AAA-GGAAAATGATAGAGAGT
1 AATCAGTAAAATGGAAAAGGATAAAGAGT
10654 AA
1 AA
10656 AATATTAACC
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:0.53, C:0.03, G:0.24, T:0.19
Consensus pattern (29 bp):
AATCAGTAAAATGGAAAAGGATAAAGAGT
Found at i:10727 original size:57 final size:57
Alignment explanation
Indices: 10666--10778 Score: 131
Period size: 57 Copynumber: 2.0 Consensus size: 57
10656 AATATTAACC
*
10666 AGTAA-AAGGTAA-AGGCAATCAGTAAAGAATAAAATATTAATCAGTAAAGAGTAAAAT
1 AGTAATAA-GTAAGAGGCAATCAGT-AAGAATAAAATAGTAATCAGTAAAGAGTAAAAT
* * * * **
10723 AGTAATCAGTAAGTGGTAATTAGTAAGCGTAAAATAGTAATCAGTAAAGAGTAAAA
1 AGTAATAAGTAAGAGGCAATCAGTAAGAATAAAATAGTAATCAGTAAAGAGTAAAA
10779 GGTGATCAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
57 38 0.81
58 9 0.19
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.23
Consensus pattern (57 bp):
AGTAATAAGTAAGAGGCAATCAGTAAGAATAAAATAGTAATCAGTAAAGAGTAAAAT
Found at i:10741 original size:22 final size:22
Alignment explanation
Indices: 10649--10734 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
10639 AAAATGATAG
* *
10649 AGAGTAAAATATTAACCAGTAA
1 AGAGTAAAATAGTAATCAGTAA
* *
10671 A-AGGT-AAA-GGCAATCAGTAA
1 AGA-GTAAAATAGTAATCAGTAA
* *
10691 AGAATAAAATATTAATCAGTAA
1 AGAGTAAAATAGTAATCAGTAA
10713 AGAGTAAAATAGTAATCAGTAA
1 AGAGTAAAATAGTAATCAGTAA
10735 GTGGTAATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
20 10 0.20
21 8 0.16
22 32 0.64
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.22
Consensus pattern (22 bp):
AGAGTAAAATAGTAATCAGTAA
Found at i:10762 original size:21 final size:22
Alignment explanation
Indices: 10738--10778 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10728 TCAGTAAGTG
* *
10738 GTAATTAGT-AAGCGTAAAATA
1 GTAATCAGTAAAGAGTAAAATA
10759 GTAATCAGTAAAGAGTAAAA
1 GTAATCAGTAAAGAGTAAAA
10779 GGTGATCAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (22 bp):
GTAATCAGTAAAGAGTAAAATA
Found at i:12580 original size:27 final size:27
Alignment explanation
Indices: 12550--12602 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
12540 TAGGGTCATC
12550 CAGGGGCATTTTGGTCATTTTCACATT
1 CAGGGGCATTTTGGTCATTTTCACATT
12577 CAGGGGCATTTTGGTCATTTTCACAT
1 CAGGGGCATTTTGGTCATTTTCACAT
12603 AAGGGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTTCACATT
Found at i:12622 original size:25 final size:27
Alignment explanation
Indices: 12553--12622 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
12543 GGTCATCCAG
*
12553 GGGCATTTTGGTCATTTTCACATTCAG
1 GGGCATTTTGGTCATTTTCACATTCAA
12580 GGGCATTTTGGTCATTTTCACA-T-AA
1 GGGCATTTTGGTCATTTTCACATTCAA
* *
12605 GGGTATTTTGGTCTTTTT
1 GGGCATTTTGGTCATTTT
12623 TGACTCCACT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 17 0.43
26 1 0.03
27 22 0.55
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTCACATTCAA
Found at i:17024 original size:36 final size:38
Alignment explanation
Indices: 16930--17029 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 38
16920 TTTAAGCAAT
16930 TCCAAGAGAAGACTTTTGGAAAATAAATGTTTTTTAGCAAA
1 TCCAAGAGAAGACTTTTGG-AAATAAATG-TTTTTA-CAAA
* *
16971 ACCAAAAGAAGACTTTTGGAAATAAATG-TTTTA-AAA
1 TCCAAGAGAAGACTTTTGGAAATAAATGTTTTTACAAA
17007 TCCAAGAGAAGACTTTTGGAAAT
1 TCCAAGAGAAGACTTTTGGAAAT
17030 TAATAAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
36 24 0.44
38 5 0.09
40 9 0.16
41 17 0.31
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (38 bp):
TCCAAGAGAAGACTTTTGGAAATAAATGTTTTTACAAA
Found at i:24024 original size:6 final size:6
Alignment explanation
Indices: 24013--24039 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24003 TATAATCTGC
24013 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
24040 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:27846 original size:42 final size:43
Alignment explanation
Indices: 27800--27886 Score: 124
Period size: 42 Copynumber: 2.0 Consensus size: 43
27790 CGCCATCTGT
*
27800 GCAGCCTGCCC-GGCCATGCTCGGCCTTGCCCGCTCCT-GCCGC
1 GCAGCC-GCCCAGGCCATGCTCGGCCTTGCCCGCACCTAGCCGC
* *
27842 GCAGCCGCCCATGCCATGCTCGGCCTTGTCCGCACCTAGCCGC
1 GCAGCCGCCCAGGCCATGCTCGGCCTTGCCCGCACCTAGCCGC
27885 GC
1 GC
27887 CACCAGCACC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 4 0.10
42 29 0.73
43 7 0.17
ACGTcount: A:0.08, C:0.48, G:0.28, T:0.16
Consensus pattern (43 bp):
GCAGCCGCCCAGGCCATGCTCGGCCTTGCCCGCACCTAGCCGC
Found at i:30225 original size:10 final size:10
Alignment explanation
Indices: 30210--30234 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30200 GTTGCTGCTT
30210 AATTCCAGAA
1 AATTCCAGAA
30220 AATTCCAGAA
1 AATTCCAGAA
30230 AATTC
1 AATTC
30235 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:31198 original size:6 final size:6
Alignment explanation
Indices: 31187--31213 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31177 TATAATCTGC
31187 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
31214 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:32239 original size:15 final size:16
Alignment explanation
Indices: 32219--32248 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32209 TGTAAGTTAA
32219 TCAAAA-ATCAATTTT
1 TCAAAAGATCAATTTT
32234 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
32249 GAATTCACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (16 bp):
TCAAAAGATCAATTTT
Found at i:43517 original size:18 final size:19
Alignment explanation
Indices: 43483--43527 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
43473 TGAAGATTTC
*
43483 TTGAAGATAATTTGAAGAT
1 TTGAAGATAATTTGAAGAA
*
43502 TTGAAGATCA-TTGAAGAA
1 TTGAAGATAATTTGAAGAA
43520 TTGAAGAT
1 TTGAAGAT
43528 TGGAGCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.33
Consensus pattern (19 bp):
TTGAAGATAATTTGAAGAA
Found at i:45259 original size:17 final size:17
Alignment explanation
Indices: 45237--45269 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
45227 GCCGAGGTGC
45237 GTGATCCTTTACTTGAA
1 GTGATCCTTTACTTGAA
45254 GTGATCCTTTACTTGA
1 GTGATCCTTTACTTGA
45270 TGATCTCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (17 bp):
GTGATCCTTTACTTGAA
Found at i:54433 original size:22 final size:22
Alignment explanation
Indices: 54384--54426 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
54374 AGCTCATTCG
*
54384 AATTTCTGAAATTGAATTACAC
1 AATTTATGAAATTGAATTACAC
54406 AATTTATGAAATTGAATTACA
1 AATTTATGAAATTGAATTACA
54427 TTATTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (22 bp):
AATTTATGAAATTGAATTACAC
Done.