Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013553.1 Corchorus capsularis cultivar CVL-1 contig13574, 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: 53407
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--83 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
1 C
2 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
44 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
84 TTAAAATTTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5065 original size:47 final size:46
Alignment explanation
Indices: 4978--5066 Score: 115
Period size: 47 Copynumber: 1.9 Consensus size: 46
4968 TAGAAAGTAA
*
4978 GTTCTATAATAACTTAGTTTACATGCAACTAGATTTTTTAATTTTG
1 GTTCTATAATAACTTAGTTTACATGCAACTAGATTATTTAATTTTG
* * ** *
5024 GTTCTGTAGTAACTTAGTTTTACATGTTACTGGATTATTTAAT
1 GTTCTATAATAACTTAG-TTTACATGCAACTAGATTATTTAAT
5067 AATGTATTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 15 0.42
47 21 0.58
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.48
Consensus pattern (46 bp):
GTTCTATAATAACTTAGTTTACATGCAACTAGATTATTTAATTTTG
Found at i:8112 original size:2 final size:2
Alignment explanation
Indices: 8105--8129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8095 TAAAAACCCT
8105 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
8130 TCCCATCAAT
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:9890 original size:17 final size:17
Alignment explanation
Indices: 9868--9900 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9858 CTCAAAACCA
*
9868 TTTCCAGTAGGTGTTAT
1 TTTCCAGTAAGTGTTAT
9885 TTTCCAGTAAGTGTTA
1 TTTCCAGTAAGTGTTA
9901 ATGTACTAAA
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:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (17 bp):
TTTCCAGTAAGTGTTAT
Found at i:10252 original size:30 final size:30
Alignment explanation
Indices: 10216--10276 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
10206 ATAACGGATA
*
10216 ACATTAAGTGGTCAAATATTCAGATCAAGC
1 ACATTAAGCGGTCAAATATTCAGATCAAGC
10246 ACATTAAGCGGTCAAATATTCAGATCAAGC
1 ACATTAAGCGGTCAAATATTCAGATCAAGC
10276 A
1 A
10277 TCATCCTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (30 bp):
ACATTAAGCGGTCAAATATTCAGATCAAGC
Found at i:13160 original size:14 final size:13
Alignment explanation
Indices: 13135--13168 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
13125 AAAAAAATAA
13135 ATTTCAATAAAAAT
1 ATTT-AATAAAAAT
13149 ATTTAATAAAAAT
1 ATTTAATAAAAAT
13162 ATTTAAT
1 ATTTAAT
13169 TTTTATGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTTAATAAAAAT
Found at i:14916 original size:94 final size:94
Alignment explanation
Indices: 14755--14941 Score: 277
Period size: 94 Copynumber: 2.0 Consensus size: 94
14745 ATGTACATGG
* * *
14755 AATCTTATTGAAAATAAAGGGACCCAGTGTGCTTGAGAACTCACAATATAGATAAGGCAAACAAT
1 AATCTGATTGAAAATAAAGGGACCCAGTCTGCATGAGAACTCACAATATAGATAAGGCAAACAAT
*
14820 AGTTAAAATTAAGAGGTCTCCTTAGTTAA
66 AGTTAAAATTAAGAGGTCTCCATAGTTAA
* * * * *
14849 AATCTGATTGAAAATAAAGTGA-CCAGGTCTGGATGAGAACTCAGAATATAGATAAGGGAAAGAA
1 AATCTGATTGAAAATAAAGGGACCCA-GTCTGCATGAGAACTCACAATATAGATAAGGCAAACAA
14913 TAGTTAAAATTAAGAGGTCTCCATAGTTA
65 TAGTTAAAATTAAGAGGTCTCCATAGTTA
14942 GGAGTAGAGA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 3 0.04
94 80 0.96
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (94 bp):
AATCTGATTGAAAATAAAGGGACCCAGTCTGCATGAGAACTCACAATATAGATAAGGCAAACAAT
AGTTAAAATTAAGAGGTCTCCATAGTTAA
Found at i:16808 original size:18 final size:18
Alignment explanation
Indices: 16787--16823 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16777 AGCTGTTACC
*
16787 TAATGAAATTTTAAGACA
1 TAATGAAATTTGAAGACA
16805 TAATGAAATTTGAAGACA
1 TAATGAAATTTGAAGACA
16823 T
1 T
16824 GATTGAGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (18 bp):
TAATGAAATTTGAAGACA
Found at i:21503 original size:37 final size:37
Alignment explanation
Indices: 21453--21528 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
21443 TCTACTGTTT
* *
21453 ATTTGATTGGAGGATGAACAGTGGATTTAAGAGATTC
1 ATTTCATTCGAGGATGAACAGTGGATTTAAGAGATTC
21490 ATTTCATTCGAGGATGAACAGTGGATTTAAGAGATTC
1 ATTTCATTCGAGGATGAACAGTGGATTTAAGAGATTC
21527 AT
1 AT
21529 CTATTAGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (37 bp):
ATTTCATTCGAGGATGAACAGTGGATTTAAGAGATTC
Found at i:21549 original size:25 final size:25
Alignment explanation
Indices: 21521--21576 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
21511 TGGATTTAAG
*
21521 AGATTCATCTATTAG-TGTTTTCTTT
1 AGATTCATCT-TTAGATATTTTCTTT
**
21546 AGATGTTTTCTTTAGATATTTTCTTT
1 AGAT-TCATCTTTAGATATTTTCTTT
21572 AGATT
1 AGATT
21577 TCGATTGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.57
Consensus pattern (25 bp):
AGATTCATCTTTAGATATTTTCTTT
Found at i:21554 original size:13 final size:13
Alignment explanation
Indices: 21532--21575 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
21522 GATTCATCTA
21532 TTAG-TGTTTTCT
1 TTAGATGTTTTCT
21544 TTAGATGTTTTCT
1 TTAGATGTTTTCT
*
21557 TTAGATATTTTCT
1 TTAGATGTTTTCT
21570 TTAGAT
1 TTAGAT
21576 TTCGATTGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 4 0.13
13 26 0.87
ACGTcount: A:0.18, C:0.07, G:0.14, T:0.61
Consensus pattern (13 bp):
TTAGATGTTTTCT
Found at i:22951 original size:29 final size:29
Alignment explanation
Indices: 22919--23003 Score: 129
Period size: 27 Copynumber: 3.0 Consensus size: 29
22909 GACAACTCTT
*
22919 GATTCATGAATAATCACAATATTAATTAA
1 GATTCATGAATAATCACATTATTAATTAA
*
22948 GATTCATGAATAATCACATTATTAGTT--
1 GATTCATGAATAATCACATTATTAATTAA
*
22975 GATTCATGAATAATCACATTATTCATTAA
1 GATTCATGAATAATCACATTATTAATTAA
23004 TGTCTTTTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 25 0.50
29 25 0.50
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (29 bp):
GATTCATGAATAATCACATTATTAATTAA
Found at i:25489 original size:21 final size:22
Alignment explanation
Indices: 25465--25829 Score: 134
Period size: 22 Copynumber: 16.7 Consensus size: 22
25455 TTACTATTTC
25465 ACTGATTA-TTCTTTACTTTGT
1 ACTGATTACTTCTTTACTTTGT
25486 ACTGATTACTAT-TTTACTCTTGT
1 ACTGATTACT-TCTTTACT-TTGT
*
25509 --TGATTACCTTC-TTACTTTTT
1 ACTGATTA-CTTCTTTACTTTGT
* *
25529 ACTGATTACCAT-TTTACTCTTTT
1 ACTGATTA-CTTCTTTACT-TTGT
* * *
25552 ACTGATTACTATTTTCTGCTCCTTTTTT
1 ACTGATTAC----TTCT-TTAC-TTTGT
* *
25580 ACTGATTAC-TCTTTTAGTTTTT
1 ACTGATTACTTC-TTTACTTTGT
* *
25602 ACTGATTACCT-TTTGCGTTT-T
1 ACTGATTACTTCTTTAC-TTTGT
25623 ACTGATTATCTT-TTTACTTCT-T
1 ACTGATTA-CTTCTTTACTT-TGT
*
25645 GCTGATTAGCTT-TTTACTCTT-T
1 ACTGATTA-CTTCTTTACT-TTGT
* *
25667 ACTGATCACCTT-TTTACTCT-T
1 ACTGATTA-CTTCTTTACTTTGT
* *
25688 ACTGATTTCCT-TTTACTTCT-T
1 ACTGATTACTTCTTTACTT-TGT
* *
25709 ACTTATTACTT-TTTACTCT-T
1 ACTGATTACTTCTTTACTTTGT
* *
25729 ACTGATTAC-TATTTACTTTTT
1 ACTGATTACTTCTTTACTTTGT
*
25750 ACTGACTACTAT-TTTACTCTTGT
1 ACTGATTACT-TCTTTACT-TTGT
*
25773 --TGATTACCTTC-TTACTTTTT
1 ACTGATTA-CTTCTTTACTTTGT
*
25793 ACTGATTACTAT-TTTACTCTTTT
1 ACTGATTACT-TCTTTACT-TTGT
25816 ACTGATTAC-TCTTT
1 ACTGATTACTTCTTT
25830 TTTACCCTTT
Statistics
Matches: 276, Mismatches: 32, Indels: 71
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.00
20 31 0.11
21 81 0.29
22 105 0.38
23 39 0.14
24 1 0.00
26 1 0.00
27 1 0.00
28 15 0.05
29 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.55
Consensus pattern (22 bp):
ACTGATTACTTCTTTACTTTGT
Found at i:25536 original size:43 final size:42
Alignment explanation
Indices: 25476--25813 Score: 281
Period size: 43 Copynumber: 7.7 Consensus size: 42
25466 CTGATTATTC
*
25476 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
* * *
25518 TCTTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTACTATTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTTGT--TGATTAC---CT
* * * *
25566 TCTGCTCCTTTTTTACTGATTACTCTTTTAGT-TTTTACTGATTACCT
1 T-T--TAC-TTTTTACTGATTACTATTTTACTCTTGT--TGATTACCT
* * * *
25613 TTTGCGTTTTACTGATTATCT-TTTTACTTCTTGCTGATTAGCTT
1 TTTACTTTTTACTGATTA-CTATTTTAC-TCTTGTTGATTA-CCT
* * ** *
25657 TTTACTCTTTACTGATCACCT-TTTTACTCTTACTGATTTCCT
1 TTTACTTTTTACTGATTA-CTATTTTACTCTTGTTGATTACCT
* * **
25699 TTTACTTCTTACTTATTACT-TTTTACTCTTACTGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
*
25739 ATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
25782 TCTTACTTTTTACTGATTACTATTTTACTCTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTT
25814 TTACTGATTA
Statistics
Matches: 245, Mismatches: 34, Indels: 33
0.79 0.11 0.11
Matches are distributed among these distances:
40 2 0.01
41 36 0.15
42 34 0.14
43 93 0.38
44 29 0.12
45 9 0.04
46 1 0.00
47 2 0.01
48 4 0.02
50 15 0.06
51 20 0.08
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.56
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
Found at i:25560 original size:15 final size:15
Alignment explanation
Indices: 25542--25595 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
25532 GATTACCATT
25542 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
25557 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
25570 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
25585 TTACTCTTTTA
1 TTACTCTTTTA
25596 GTTTTTACTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 17 0.57
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:26174 original size:54 final size:54
Alignment explanation
Indices: 26052--26256 Score: 260
Period size: 54 Copynumber: 3.8 Consensus size: 54
26042 CATTTTAACT
* *
26052 CTTAATTA-TCGATTTACTGATTACTATTACT-TTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTTCTATTACTCTTGAC-CTGATTAATTTC-TTTTA
*
26107 CTTAATTACTGATTTACTGATTTCTATTACTCTTTA-CTGATTAATTTCTTTTCA
1 CTTAATTACTGATTTACTGATTTCTATTACTCTTGACCTGATTAATTTCTTTT-A
* * *
26161 CTTAATTATTGATTTACTGATTTCTATCAC-CTTGACTCTAATTAATTT-TTTTA
1 CTTAATTACTGATTTACTGATTTCTATTACTCTTGAC-CTGATTAATTTCTTTTA
*
26214 CTTAATTACTGATTTACTGATTTCTATTACTCTTTA-CTGATTA
1 CTTAATTACTGATTTACTGATTTCTATTACTCTTGACCTGATTA
26257 TCACTTTACT
Statistics
Matches: 133, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
52 6 0.05
53 37 0.28
54 48 0.36
55 38 0.29
56 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.52
Consensus pattern (54 bp):
CTTAATTACTGATTTACTGATTTCTATTACTCTTGACCTGATTAATTTCTTTTA
Found at i:26248 original size:107 final size:109
Alignment explanation
Indices: 26052--26256 Score: 351
Period size: 107 Copynumber: 1.9 Consensus size: 109
26042 CATTTTAACT
* * *
26052 CTTAATTATCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAATTACT
1 CTTAATTATCGATTTACTGATTACTATCACCTTGACTCTAATTAATCTCTTTTTACTTAATTACT
26117 GATTTACTGATTTCTATTACTCTTTACTGATTAATTTCTTTTCA
66 GATTTACTGATTTCTATTACTCTTTACTGATTAATTTCTTTTCA
* *
26161 CTTAATTATTGATTTACTGATTTCTATCACCTTGACTCTAATTAAT-T-TTTTTACTTAATTACT
1 CTTAATTATCGATTTACTGATTACTATCACCTTGACTCTAATTAATCTCTTTTTACTTAATTACT
26224 GATTTACTGATTTCTATTACTCTTTACTGATTA
66 GATTTACTGATTTCTATTACTCTTTACTGATTA
26257 TCACTTTACT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
107 49 0.54
108 1 0.01
109 41 0.45
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.52
Consensus pattern (109 bp):
CTTAATTATCGATTTACTGATTACTATCACCTTGACTCTAATTAATCTCTTTTTACTTAATTACT
GATTTACTGATTTCTATTACTCTTTACTGATTAATTTCTTTTCA
Found at i:26268 original size:22 final size:22
Alignment explanation
Indices: 26240--26301 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
26230 CTGATTTCTA
*
26240 TTACTCTTTACTGATTATCACT
1 TTACTCTTTACTGATTACCACT
* *
26262 TTACTCTTTACTGATTGCCGCT
1 TTACTCTTTACTGATTACCACT
26284 TTAC-CTTTTACTGATTAC
1 TTACTC-TTTACTGATTAC
26302 ATCTTTCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.48
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCACT
Found at i:26360 original size:30 final size:31
Alignment explanation
Indices: 26293--26352 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
26283 TTTACCTTTT
26293 ACTGATTACATCTTTCTTATTGAACTTAATC
1 ACTGATTACATCTTTCTTATTGAACTTAATC
*
26324 ACTGATTAC-TTTTTCTTATTGAACTTAAT
1 ACTGATTACATCTTTCTTATTGAACTTAAT
26353 TGCTGATTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (31 bp):
ACTGATTACATCTTTCTTATTGAACTTAATC
Found at i:26370 original size:30 final size:30
Alignment explanation
Indices: 26306--26384 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
26296 GATTACATCT
***
26306 TTCTTATTGAACTTAATCACTGATTACTTT
1 TTCTTATTGAACTTAATCACTGATTACCCC
** *
26336 TTCTTATTGAACTTAATTGCTGATTGCCCC
1 TTCTTATTGAACTTAATCACTGATTACCCC
*
26366 TTC-T-TGGAACTTAATCACT
1 TTCTTATTGAACTTAATCACT
26385 CTCATAACCC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
28 12 0.30
29 1 0.03
30 27 0.68
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (30 bp):
TTCTTATTGAACTTAATCACTGATTACCCC
Found at i:32756 original size:29 final size:29
Alignment explanation
Indices: 32724--32808 Score: 138
Period size: 27 Copynumber: 3.0 Consensus size: 29
32714 GACAACTCTT
*
32724 GATTCATGAATAATCACAATATTAATTAA
1 GATTCATGAATAATCACATTATTAATTAA
32753 GATTCATGAATAATCACATTATTAATT--
1 GATTCATGAATAATCACATTATTAATTAA
*
32780 GATTCATGAATAATCACATTATTCATTAA
1 GATTCATGAATAATCACATTATTAATTAA
32809 TGTCTTTTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
27 26 0.50
29 26 0.50
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38
Consensus pattern (29 bp):
GATTCATGAATAATCACATTATTAATTAA
Found at i:32791 original size:27 final size:27
Alignment explanation
Indices: 32722--32802 Score: 135
Period size: 29 Copynumber: 2.9 Consensus size: 27
32712 AAGACAACTC
*
32722 TTGATTCATGAATAATCACAATATTAA
1 TTGATTCATGAATAATCACATTATTAA
32749 TTAAGATTCATGAATAATCACATTATTAA
1 TT--GATTCATGAATAATCACATTATTAA
32778 TTGATTCATGAATAATCACATTATT
1 TTGATTCATGAATAATCACATTATT
32803 CATTAATGTC
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
27 25 0.49
29 26 0.51
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (27 bp):
TTGATTCATGAATAATCACATTATTAA
Found at i:33754 original size:22 final size:22
Alignment explanation
Indices: 33704--33821 Score: 102
Period size: 22 Copynumber: 5.4 Consensus size: 22
33694 AGGAGTACCA
*
33704 AAATTTGATAGA-A-GATTATC
1 AAATTTCATAGAGATGATTATC
*
33724 AAATCTCATAGAG-TGATTATC
1 AAATTTCATAGAGATGATTATC
33745 GAAATTTCATAGAGATCAGATTATC
1 -AAATTTCATAGAGAT--GATTATC
* *
33770 AAATTTTATAG-GAAGATTATC
1 AAATTTCATAGAGATGATTATC
* *
33791 AAAATTTCATAGTGTTG-TTATC
1 -AAATTTCATAGAGATGATTATC
33813 AAAATTTCA
1 -AAATTTCA
33822 AAGCGAGGTT
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
20 10 0.12
21 14 0.17
22 36 0.44
23 5 0.06
24 10 0.12
25 7 0.09
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
AAATTTCATAGAGATGATTATC
Found at i:33855 original size:22 final size:22
Alignment explanation
Indices: 33717--33955 Score: 102
Period size: 22 Copynumber: 10.8 Consensus size: 22
33707 TTTGATAGAA
*
33717 GATTATC-AAATCTCATAGA-GT
1 GATTATCAAAATTTCATA-ATGT
*
33738 GATTATCGAAATTTCATAGA-GAT
1 GATTATCAAAATTTCATA-ATG-T
* * *
33761 CAGATTATC-AAATTTTAT-AGGAA
1 --GATTATCAAAATTTCATAATG-T
*
33784 GATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAATG-T
*
33807 G-TTATCAAAATTTCA-AA-GC
1 GATTATCAAAATTTCATAATGT
*
33826 GAGGTTATCAAAATTACATAATGT
1 GA--TTATCAAAATTTCATAATGT
* * * *
33850 GATTATTAGAATTTCATAAAGG
1 GATTATCAAAATTTCATAATGT
* * * * * *
33872 GGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCATAATGT
* * *
33894 GGTTATCAAAATTTCATAAAGA
1 GATTATCAAAATTTCATAATGT
* *
33916 GGTTATC-AAATTTCCAAAATGT
1 GATTATCAAAATTT-CATAATGT
33938 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
33956 GTGATATTTC
Statistics
Matches: 171, Mismatches: 32, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 22 0.13
22 116 0.68
23 13 0.08
24 11 0.06
25 7 0.04
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
GATTATCAAAATTTCATAATGT
Found at i:34060 original size:20 final size:20
Alignment explanation
Indices: 34037--34088 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
34027 TTATGAGGTA
*
34037 ATCAAAATTTCACGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
34057 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
34077 ATCAAAATTTCA
1 ATCAAAATTTCA
34089 TAGTTTAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:39826 original size:19 final size:18
Alignment explanation
Indices: 39802--39837 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39792 TGAAGATTTC
39802 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
39821 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
39838 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:41138 original size:15 final size:16
Alignment explanation
Indices: 41118--41151 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41108 GATTGCCCTC
*
41118 TTAGTT-AATTTACTT
1 TTAGTTAAATTTAATT
41133 TTAGTTAAATTTAATT
1 TTAGTTAAATTTAATT
41149 TTA
1 TTA
41152 ATTCCTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
TTAGTTAAATTTAATT
Found at i:43624 original size:19 final size:19
Alignment explanation
Indices: 43588--43647 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
43578 ATATAAGCAT
43588 CAAAACCCAAACATAAATGA
1 CAAAACCCAAA-ATAAATGA
* *
43608 CAAAACCCAAGATAAATCA
1 CAAAACCCAAAATAAATGA
43627 -ATAAAGCCCAAAATAAATGA
1 CA-AAA-CCCAAAATAAATGA
43647 C
1 C
43648 TGAGCCCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 10 0.30
20 22 0.67
ACGTcount: A:0.58, C:0.23, G:0.07, T:0.12
Consensus pattern (19 bp):
CAAAACCCAAAATAAATGA
Found at i:48778 original size:49 final size:46
Alignment explanation
Indices: 48667--48804 Score: 143
Period size: 48 Copynumber: 2.9 Consensus size: 46
48657 CCGAGCGTGC
* ** ***
48667 CAATTTTGTCCA-AAAATTGATAAAAAGTGCAATAAAAAGTAAATATT
1 CAATTTTGT-CATAAAATTGAGAAAAAGTGCAGGAAAAA-TAAAGGGT
48714 CAATTTTGTCATAAAAATTGAGAAAAAGGTGCGAGGAAAAATAAAGGGT
1 CAATTTTGTCAT-AAAATTGAGAAAAA-GTGC-AGGAAAAATAAAGGGT
** *
48763 CAATTTTGTTGTAAAATTGAGAAAAAGTGCAGGAAAAGTAAA
1 CAATTTTGTCATAAAATTGAGAAAAAGTGCAGGAAAAATAAA
48805 TGATTGCTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
46 13 0.17
47 13 0.17
48 27 0.35
49 19 0.24
50 6 0.08
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (46 bp):
CAATTTTGTCATAAAATTGAGAAAAAGTGCAGGAAAAATAAAGGGT
Found at i:49138 original size:27 final size:27
Alignment explanation
Indices: 49102--49165 Score: 103
Period size: 27 Copynumber: 2.3 Consensus size: 27
49092 ATTTCTGGAA
49102 AACAAGGGAAATG-GACAATTAAAAAGG
1 AACAAGGGAAA-GAGACAATTAAAAAGG
49129 AACAAGGGAAAGAGACAATTAAAAAGG
1 AACAAGGGAAAGAGACAATTAAAAAGG
49156 AACAGAGGGA
1 AACA-AGGGA
49166 GTAATCTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.03
27 29 0.83
28 5 0.14
ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (27 bp):
AACAAGGGAAAGAGACAATTAAAAAGG
Found at i:50167 original size:30 final size:30
Alignment explanation
Indices: 50132--50193 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
50122 TATAATTTTT
50132 AATCATTAAACTTTTATTTATTAATTATAA
1 AATCATTAAACTTTTATTTATTAATTATAA
*
50162 AATCATTATACTTTTATTTATTAATTATAA
1 AATCATTAAACTTTTATTTATTAATTATAA
50192 AA
1 AA
50194 AGACATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (30 bp):
AATCATTAAACTTTTATTTATTAATTATAA
Found at i:53362 original size:2 final size:2
Alignment explanation
Indices: 53355--53386 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53345 TTCATTAACT
53355 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
53387 ACTTGGTATT
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
Done.