Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024448.1 Corchorus olitorius cultivar O-4 contig24481, 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: 68587
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3739 original size:20 final size:19
Alignment explanation
Indices: 3701--3740 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
3691 GTTTTGTGTT
*
3701 TTGCGTTTTTGAAAAAAAA
1 TTGCGTTTTAGAAAAAAAA
3720 TTGCGTTTTCAGATAAAAAAA
1 TTGCGTTTT-AGA-AAAAAAA
3741 ATTCTCTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (19 bp):
TTGCGTTTTAGAAAAAAAA
Found at i:7259 original size:18 final size:19
Alignment explanation
Indices: 7225--7263 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
7215 TGAAGTTTTG
7225 TTGAAGATAATTTGAAGAA
1 TTGAAGATAATTTGAAGAA
*
7244 TTGAAGATTA-TTGAAGAA
1 TTGAAGATAATTTGAAGAA
7262 TT
1 TT
7264 ATTTCAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (19 bp):
TTGAAGATAATTTGAAGAA
Found at i:7722 original size:22 final size:22
Alignment explanation
Indices: 7694--7737 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
7684 GTCATTTTCT
7694 AATTCACTTTTGGCATCTAGTA
1 AATTCACTTTTGGCATCTAGTA
*
7716 AATTCACTTTTGGCATTTAGTA
1 AATTCACTTTTGGCATCTAGTA
7738 TAAAATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (22 bp):
AATTCACTTTTGGCATCTAGTA
Found at i:11472 original size:45 final size:45
Alignment explanation
Indices: 11373--11481 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
11363 AAAGTTTTCG
* * * *
11373 TTTTTGGGAAAGTCCCCATTAATGCATTTTCAAAAAATCGATTTA
1 TTTTAGGGAAAGTTCCCATCAAAGCATTTTCAAAAAATCGATTTA
* * * *
11418 TTTTAGGGAAAGTTCCCATCAAAGCATTTTC-AAAAGTTGTTTTT
1 TTTTAGGGAAAGTTCCCATCAAAGCATTTTCAAAAAATCGATTTA
11462 TTTTACGGGAAAGTTCCCAT
1 TTTTA-GGGAAAGTTCCCAT
11482 TGAAGTTTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 14 0.25
45 41 0.75
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (45 bp):
TTTTAGGGAAAGTTCCCATCAAAGCATTTTCAAAAAATCGATTTA
Found at i:11599 original size:65 final size:66
Alignment explanation
Indices: 11518--11881 Score: 236
Period size: 67 Copynumber: 5.5 Consensus size: 66
11508 AGCATTTTCT
* * *
11518 TTTTCCAAAAATACCCTTTCGATCGAAGGGTAAGTTTCATCTTTTTCGTGTCTAAG-TTAGTTGT
1 TTTTCCAAAAATACCCTTTCGGTCGAAGGGTAAGTTTCATATTTTTCGTATCTAAGTTTAGTTGT
11582 C
66 C
* * * * *
11583 TTTTCCTAAAACACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCGTATCTAAGTTTAGTTTT
1 TTTTCCAAAAATACCCTTTCGGTCGAAGGGTAAGTTTCATATTTTTCGTATCTAAGTTTAGTTGT
11648 C
66 C
* * * * * * *
11649 TTTTCCAAAAAATAACCTTTCGGTCGAAGGGT-CGTTT-TTGTCTTTT-GCATTTGAGTTTAGTA
1 TTTTCC-AAAAATACCCTTTCGGTCGAAGGGTAAGTTTCATAT-TTTTCGTATCTAAGTTTAG--
*
11711 TTTTC
62 TTGTC
* * * * * * * * * * *
11716 ATTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTT-GCATTTGAGTTTAGTATT
1 TTTTCCAAAAATACCCTTTCGGTCGAAGGGTAAGTTTCATATTTTTCGTATCTAAGTTTAG--TT
*
11780 TTC
64 GTC
* * * * * * * * * * *
11783 ATTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTCCTCTTTTT-GCATTTGAGTTTAGTATT
1 TTTTCCAAAAATACCCTTTCGGTCGAAGGGTAAGTTTCATATTTTTCGTATCTAAGTTTAG--TT
*
11847 TTC
64 GTC
*
11850 GTTTTCCAAAAATACCCTTTCGGTCAAAGGGT
1 -TTTTCCAAAAATACCCTTTCGGTCGAAGGGT
11882 CGTTTTTGTC
Statistics
Matches: 260, Mismatches: 31, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
65 62 0.24
66 43 0.17
67 125 0.48
68 30 0.12
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (66 bp):
TTTTCCAAAAATACCCTTTCGGTCGAAGGGTAAGTTTCATATTTTTCGTATCTAAGTTTAGTTGT
C
Found at i:11715 original size:67 final size:67
Alignment explanation
Indices: 11596--12210 Score: 508
Period size: 67 Copynumber: 9.2 Consensus size: 67
11586 TCCTAAAACA
* ** * * * * * *
11596 CCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCGTATCTAAGTTTAG--TTTTCTTTTCCAAAA
1 CCCTTTCGGTCAAAGGGTCATTTTTGTCTTTTT-GCATTTGAGTTTAGTATTTTCATTTCC-AAG
*
11659 AATA
64 AATG
* * *
11663 ACCTTTCGGTCGAAGGGTCGTTTTTGTC-TTTTGCATTTGAGTTTAGTATTTTCATTTCCAAGAA
1 CCCTTTCGGTCAAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTTAGTATTTTCATTTCCAAGAA
11727 TG
66 TG
*
11729 CCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTGAGTTTAGTATTTTCATTTCCAAGAA
1 CCCTTTCGGTCAAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTTAGTATTTTCATTTCCAAGAA
11794 TG
66 TG
** * *
11796 CCCTTTCGGTCAAAGGGTCATTTTCCTCTTTTTGCATTTGAGTTTAGTATTTTCGTTTTCCAAAA
1 CCCTTTCGGTCAAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTTAGTATTTTC-ATTTCCAAGA
*
11861 ATA
65 ATG
*
11864 CCCTTTCGGTCAAAGGGTCGTTTTTGTC-TTTTGCATTTGAGTTTAGTATTTTCATTTCCAAGAA
1 CCCTTTCGGTCAAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTTAGTATTTTCATTTCCAAGAA
11928 TG
66 TG
* * * * * *
11930 CCCTTTCGGTCAAAGGGTCATTTTTATACATTTCTGCATCTAAGTTTAGCT-TTGTC--TACCAA
1 CCCTTTCGGTCAAAGGGTCATTTTTGT-C-TTTTTGCATTTGAGTTTAG-TATTTTCATTTCC-A
*
11992 AAAATG
62 AGAATG
* * * * ** * * * *
11998 CCCCTTT-AGTGAAAGGTTCAGTTTCATAATTTTCGCATTTGAG-TT--TACTTACAATTTCCAA
1 -CCCTTTCGGTCAAAGGGTCATTTTTGT-CTTTTTGCATTTGAGTTTAGTATTTTC-ATTTCC-A
* *
12059 AAAATA
62 AGAATG
* * * **
12065 CCCTTTCGGTCAAAGGGTCAATTCTGTCATTCTTGCATTTGAGTTTA-T-TTTTGGTTTCCAA-A
1 CCCTTTCGGTCAAAGGGTCATTTTTGTC-TTTTTGCATTTGAGTTTAGTATTTTCATTTCCAAGA
*
12127 ATA
65 ATG
* ** * * * * *
12130 CCCTTTCGGTGAAAGGGTCATTTTCATCATTTTCGCATTTCAGTTTA-T-TCTAC-TTTCCAAAA
1 CCCTTTCGGTCAAAGGGTCATTTTTGTC-TTTTTGCATTTGAGTTTAGTATTTTCATTTCCAAGA
12192 ATG
65 ATG
*
12195 CCCTTTTGGTCAAAGG
1 CCCTTTCGGTCAAAGG
12211 ACAAGCTTTG
Statistics
Matches: 451, Mismatches: 78, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
63 1 0.00
64 9 0.02
65 74 0.16
66 78 0.17
67 201 0.45
68 61 0.14
69 26 0.06
70 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.43
Consensus pattern (67 bp):
CCCTTTCGGTCAAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTTAGTATTTTCATTTCCAAGAA
TG
Found at i:11882 original size:201 final size:200
Alignment explanation
Indices: 11519--12210 Score: 716
Period size: 201 Copynumber: 3.5 Consensus size: 200
11509 GCATTTTCTT
* * * * * * *
11519 TTTCCAAAAATACCCTTTCGATCGAAGGGTAAGTTTCATC-TTTTT-CGTGTCTAAG-TTAG-TT
1 TTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTCATCATTTTTGCAT-T-TAAGTTTAGTTT
* * ** * * *
11580 GTCTTTTCCTAAAACACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCGTATCTAAGTTTAG-
64 TTC-TTTCCAAAAATGCCCTTTCGGTCAAAGGGTCAGTTTCATATTTTT-GCATTTGAGTTTAGT
* *
11644 -TTTTCTTTTCCAAAAAATAACCTTTCGGTCGAAGGGTCGTTTTTGTCTTTTGCATTTGAGTTTA
127 ATTTTCTTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCGTTTTTGTCTTTTGCATTTGAGTTTA
11708 GTATTTTCA
192 GTATTTTCA
* *
11717 TTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTCGTC-TTTTTGCATTTGAGTTTAGTATTT
1 TTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTCATCATTTTTGCATTTAAGTTTAGT-TTT
* * * *
11781 TCATTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTCCTCTTTTTGCATTTGAGTTTAGTAT
65 TC-TTTCCAAAAATGCCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTGCATTTGAGTTTAGTAT
11846 TTTCGTTTTCC-AAAAATACCCTTTCGGTCAAAGGGTCGTTTTTGTCTTTTGCATTTGAGTTTAG
129 TTTC-TTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCGTTTTTGTCTTTTGCATTTGAGTTTAG
11910 TATTTTCA
193 TATTTTCA
* * *
11918 TTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTTATACATTTCTGCATCTAAGTTTAGCTTT
1 TTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTCAT-CATTTTTGCATTTAAGTTTAG-TTT
* * * * * *
11983 GTC-TACCAAAAAATGCCCCTTT-AGTGAAAGGTTCAGTTTCATAATTTTCGCATTTGAG-TT--
64 TTCTTTCC-AAAAATG-CCCTTTCGGTCAAAGGGTCAGTTTCAT-ATTTTTGCATTTGAGTTTAG
* * * ** *
12043 TACTTACAATTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAATTCTGTCATTCTTGCATTTGAG
126 TATTTTC-TTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCGTTTTTGTC-TT-TTGCATTTGAG
**
12108 TTTA-T-TTTTGG
188 TTTAGTATTTTCA
* * * * * *
12119 TTTCCAA-AATACCCTTTCGGTGAAAGGGTCATTTTCATCATTTTCGCATTTCAGTTTA-TTCTA
1 TTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTCATCATTTTTGCATTTAAGTTTAGTTTTT
*
12182 CTTTCCAAAAATGCCCTTTTGGTCAAAGG
66 CTTTCCAAAAATGCCCTTTCGGTCAAAGG
12211 ACAAGCTTTG
Statistics
Matches: 416, Mismatches: 60, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
196 6 0.01
197 20 0.05
198 46 0.11
199 29 0.07
200 80 0.19
201 147 0.35
202 33 0.08
203 54 0.13
204 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (200 bp):
TTTCCAAGAATGCCCTTTCGGTCAAAGGGTCATTTTCATCATTTTTGCATTTAAGTTTAGTTTTT
CTTTCCAAAAATGCCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTGCATTTGAGTTTAGTATTT
TCTTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCGTTTTTGTCTTTTGCATTTGAGTTTAGTAT
TTTCA
Found at i:15550 original size:29 final size:29
Alignment explanation
Indices: 15513--15573 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
15503 ACCTTTGTTT
15513 TTGTATTTGTTCAAGTGCGGGTTGTGCAC
1 TTGTATTTGTTCAAGTGCGGGTTGTGCAC
* *
15542 TTGTGTTTGTTCAAGTGTGGGTTGTGCAC
1 TTGTATTTGTTCAAGTGCGGGTTGTGCAC
15571 TTG
1 TTG
15574 GGATTGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (29 bp):
TTGTATTTGTTCAAGTGCGGGTTGTGCAC
Found at i:15594 original size:30 final size:29
Alignment explanation
Indices: 15519--15581 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
15509 GTTTTTGTAT
* * *
15519 TTGTTCAAGTGCGGGTTGTGCACTTGTGT
1 TTGTTCAAGTGTGGGTTGTGCACTTGGGA
15548 TTGTTCAAGTGTGGGTTGTGCACTTGGGA
1 TTGTTCAAGTGTGGGTTGTGCACTTGGGA
15577 TTGTT
1 TTGTT
15582 TTGAGTGTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.11, C:0.11, G:0.35, T:0.43
Consensus pattern (29 bp):
TTGTTCAAGTGTGGGTTGTGCACTTGGGA
Found at i:15628 original size:14 final size:14
Alignment explanation
Indices: 15609--15646 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
15599 CTCGGTGTCA
15609 AAGCTTTGGGTTTG
1 AAGCTTTGGGTTTG
15623 AAGCTTTGGGTTTG
1 AAGCTTTGGGTTTG
15637 AAGCTTTGGG
1 AAGCTTTGGG
15647 ATTGTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.16, C:0.08, G:0.37, T:0.39
Consensus pattern (14 bp):
AAGCTTTGGGTTTG
Found at i:23989 original size:29 final size:29
Alignment explanation
Indices: 23931--23990 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
23921 TTTGCATCTA
* *
23931 TTCAAGTGCGGGTTGTGCACTTGTGTTTG
1 TTCAAGTGCGGGTTGTGCACTTGGGATTG
*
23960 TTCAAGTGTGGGTTGTGCACTTGGGATTG
1 TTCAAGTGCGGGTTGTGCACTTGGGATTG
23989 TT
1 TT
23991 TTGAGTGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.12, C:0.12, G:0.35, T:0.42
Consensus pattern (29 bp):
TTCAAGTGCGGGTTGTGCACTTGGGATTG
Found at i:27634 original size:24 final size:24
Alignment explanation
Indices: 27603--27651 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
27593 GGGATGTATC
* *
27603 ATCGGAGGTGTGAGATTCCATACT
1 ATCGGAGGTGTAAAATTCCATACT
27627 ATCGGAGGTGTAAAATTCCATACT
1 ATCGGAGGTGTAAAATTCCATACT
27651 A
1 A
27652 AGGAAAGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (24 bp):
ATCGGAGGTGTAAAATTCCATACT
Found at i:33136 original size:11 final size:11
Alignment explanation
Indices: 33117--33153 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
33107 TGAAATGTGC
*
33117 ATTTAAATCAA
1 ATTTTAATCAA
33128 ATTTTAATCAA
1 ATTTTAATCAA
*
33139 ATTTTTATCAA
1 ATTTTAATCAA
33150 ATTT
1 ATTT
33154 AACCACTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTTAATCAA
Found at i:34642 original size:15 final size:14
Alignment explanation
Indices: 34609--34667 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
34599 CCCTTTAGTA
34609 ATTTTTT-A-TTTT
1 ATTTTTTAATTTTT
34621 A-TTTTTAATTTTT
1 ATTTTTTAATTTTT
34634 ATTTTTTTAACTTTAATT
1 A-TTTTTTAA-TTT--TT
34652 ATTTTTTAATTATTT
1 ATTTTTTAATT-TTT
34667 A
1 A
34668 ATTAATTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
11 5 0.13
12 2 0.05
13 5 0.13
15 10 0.26
16 5 0.13
17 9 0.23
18 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTTTAATTTTT
Found at i:36084 original size:218 final size:215
Alignment explanation
Indices: 35495--36355 Score: 868
Period size: 218 Copynumber: 4.0 Consensus size: 215
35485 TACAAGCGCA
* *
35495 AAAAGCGTTAACAAGAGCGACGTTATTAGAAAACATTACTCAAATTTAAAAAGAGTCGCAAGGTA
1 AAAAGCGTAAACAAGAGCGACGTTATTA-AAAA-ATTACTCAATTTTAAAAAGAGTCGCAAGGTA
* * * * *
35560 CTACAAGGTTTATTAAAAATGTCACATATTCAAACAACATTTTAAAACAATGTTGTTATAAATGT
64 CTGCGACGTTTATTAAAAATGTCACATATTAAAACAACATTTTAAAAAAATGTTGTTATAAATGT
* * * * *
35625 TGGAAAAATCTATTTTAAAAAGCGACGTTTGTT--AATAAGGTCGCATAAATGAATGACATTTGA
129 TGGAAAAATCTATATT--AAAGCGACGTTTGTTAAAAAAACGTCGCATAAATGAACGACGTTTGA
*
35688 GAAAAATATCTCTACAAACGTCGC
192 GAAAAACATCTCTACAAACGTCGC
* * * * * * *
35712 AAAATCATAAATAAAAGCGACGTCATTAAAAAATGTCACAT-AATCTTAAAAAGAGGCGCAA-G-
1 AAAAGCGTAAACAAGAGCGACGTTATTAAAAAAT-T-AC-TCAATTTTAAAAAGAGTCGCAAGGT
* ** * * **
35774 ---GCGACGTTTATTAAAAATGTCACATATTCAAATGATATTTTCAAAAAATGTAATTATAAATG
63 ACTGCGACGTTTATTAAAAATGTCACATATTAAAACAACATTTTAAAAAAATGTTGTTATAAATG
* * * * * *
35836 TTGGACAAATCTATATTATAGTGACGTTTGTTAAAAAACACATCGCATAAATCAACGACGTTTTA
128 TTGGAAAAATCTATATTAAAGCGACGTTTGTTAAAAAA-ACGTCGCATAAATGAACGACGTTTGA
* **
35901 GAAAAACGTCTCTACAAATATCGC
192 GAAAAACATCTCTACAAACGTCGC
* * *
35925 AAAAGCGTAAACACGAGCGACATTATTAAAAAATGTCACTCAATTTTCAAAAGAGTCGCAAGGTA
1 AAAAGCGTAAACAAGAGCGACGTTATTAAAAAAT-T-ACTCAATTTTAAAAAGAGTCGCAAGGTA
* * * *
35990 GTGTGACGTTTATTAAAAACGTCACATATTAAAACAACATTTTAAAAAAATGTTTTTATAAATGT
64 CTGCGACGTTTATTAAAAATGTCACATATTAAAACAACATTTTAAAAAAATGTTGTTATAAATGT
* * *
36055 T-GAAAAAGTCTATATTAAAGCGACGTTTGTTAAAAAAATGTCGTATAAATGAACGGCGTTTGAG
129 TGGAAAAA-TCTATATTAAAGCGACGTTTGTTAAAAAAACGTCGCATAAATGAACGACGTTTGAG
* *
36119 AAAAGCATCTCTATAAACGTCGC
193 AAAAACATCTCTACAAACGTCGC
* * * **
36142 AAAAGTGTAAACAAGAGCGACGTTATTGGAAAACTTATCTCGGTTTTAAAAAAGAGTCGCAAGGT
1 AAAAGCGTAAACAAGAGCGACGTTATT-AAAAAATTA-CTCAATTTT-AAAAAGAGTCGCAAGGT
* * * * *
36207 ACTGCGACGTTTATTAAAAATATCACATATTAGAATAACA---AAAAAAAACGTTGTTATAAATG
63 ACTGCGACGTTTATTAAAAATGTCACATATTAAAACAACATTTTAAAAAAATGTTGTTATAAATG
** * * * * * * *
36269 TTGGAAATGTTTATCTTAAAGTGATGTTTGTTAAAAAAATGTCGCATAAACGAAC-ATTGTTTGA
128 TTGGAAAAATCTATATTAAAGCGACGTTTGTTAAAAAAACGTCGCATAAATGAACGA-CGTTTGA
**
36333 G-AAAATGTCTCTACAAACGTCGC
192 GAAAAACATCTCTACAAACGTCGC
36356 GTTCTCACTT
Statistics
Matches: 528, Mismatches: 98, Indels: 39
0.79 0.15 0.06
Matches are distributed among these distances:
210 13 0.02
212 71 0.13
213 89 0.17
214 19 0.04
215 70 0.13
216 11 0.02
217 117 0.22
218 138 0.26
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (215 bp):
AAAAGCGTAAACAAGAGCGACGTTATTAAAAAATTACTCAATTTTAAAAAGAGTCGCAAGGTACT
GCGACGTTTATTAAAAATGTCACATATTAAAACAACATTTTAAAAAAATGTTGTTATAAATGTTG
GAAAAATCTATATTAAAGCGACGTTTGTTAAAAAAACGTCGCATAAATGAACGACGTTTGAGAAA
AACATCTCTACAAACGTCGC
Found at i:37589 original size:191 final size:191
Alignment explanation
Indices: 37258--37640 Score: 694
Period size: 191 Copynumber: 2.0 Consensus size: 191
37248 TGATAAATTT
37258 TTTACAGAGATGAGTAATTTGTGGGAAAGATTGATCTTTATTTTGGAGGTTACGAAAAGTAAATT
1 TTTACAGAGATGAGTAATTTGTGGGAAAGATTGATCTTTATTTTGGAGGTTACGAAAAGTAAATT
* * *
37323 AAATTTTGAAGCTGCGTGGCTAAAGCTTGAAGTTGACAACAAAAAATGCATTCCTACGATGTTTA
66 AAATTTTGAAGCTGCATGGCTAAAGCTTGAAGTTGACAACAAAAAACGCATTCCTACAATGTTTA
*
37388 AAGGTATGCAAATGGTGTGAGTTTTAGGATTTTCGTGTCCATTGTTAATGGAGATTGTGTG
131 AAGGTATGCAAATGGTGTGAGTTTTAGGATTTTCGTGTCCATTGTTAATGGAAATTGTGTG
*
37449 TTTACAGAGATGAGTAATTTGTGGGAAAGATTGATCTTTATTTTGGAGGTTACGAAACGTAAATT
1 TTTACAGAGATGAGTAATTTGTGGGAAAGATTGATCTTTATTTTGGAGGTTACGAAAAGTAAATT
* *
37514 AAATTTTGAAGCTGCATGGCTAAAGCTTGAAGTTGGCAACAAAAAACGCATTCCTACAATGTTTG
66 AAATTTTGAAGCTGCATGGCTAAAGCTTGAAGTTGACAACAAAAAACGCATTCCTACAATGTTTA
*
37579 AAGTTATGCAAATGGTGTGAGTTTTAGGATTTTCGTGTCCATTGTTAATGGAAATTGTGTG
131 AAGGTATGCAAATGGTGTGAGTTTTAGGATTTTCGTGTCCATTGTTAATGGAAATTGTGTG
37640 T
1 T
37641 CAATATAATT
Statistics
Matches: 184, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
191 184 1.00
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.35
Consensus pattern (191 bp):
TTTACAGAGATGAGTAATTTGTGGGAAAGATTGATCTTTATTTTGGAGGTTACGAAAAGTAAATT
AAATTTTGAAGCTGCATGGCTAAAGCTTGAAGTTGACAACAAAAAACGCATTCCTACAATGTTTA
AAGGTATGCAAATGGTGTGAGTTTTAGGATTTTCGTGTCCATTGTTAATGGAAATTGTGTG
Found at i:42842 original size:28 final size:28
Alignment explanation
Indices: 42798--42889 Score: 166
Period size: 28 Copynumber: 3.3 Consensus size: 28
42788 ATTTCAAAGT
*
42798 CGTTGCGGCAGGGTCCCCCGGACCCGCA
1 CGTTGCGACAGGGTCCCCCGGACCCGCA
*
42826 CGTTGCGACAGGATCCCCCGGACCCGCA
1 CGTTGCGACAGGGTCCCCCGGACCCGCA
42854 CGTTGCGACAGGGTCCCCCGGACCCGCA
1 CGTTGCGACAGGGTCCCCCGGACCCGCA
42882 CGTTGCGA
1 CGTTGCGA
42890 TAGCTTGGCG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.14, C:0.41, G:0.33, T:0.12
Consensus pattern (28 bp):
CGTTGCGACAGGGTCCCCCGGACCCGCA
Found at i:47646 original size:14 final size:15
Alignment explanation
Indices: 47615--47653 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
47605 TTCCCGGATG
47615 AAAAATGAAACTAAA
1 AAAAATGAAACTAAA
47630 AAAAATGAAA-TAGAA
1 AAAAATGAAACTA-AA
47645 AAAAA-GAAA
1 AAAAATGAAA
47654 AAAAAACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (15 bp):
AAAAATGAAACTAAA
Found at i:48496 original size:9 final size:9
Alignment explanation
Indices: 48450--48480 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
48440 CAAGTACATG
48450 TAAAAAAAA
1 TAAAAAAAA
*
48459 TAATAAAAA
1 TAAAAAAAA
48468 TAAAAAAAA
1 TAAAAAAAA
48477 TAAA
1 TAAA
48481 TGGAAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:48503 original size:21 final size:21
Alignment explanation
Indices: 48470--48513 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
48460 AATAAAAATA
* *
48470 AAAAAAATAAATGGA-AAAAG
1 AAAAAAAGAAATGAAGAAAAG
48490 AAAAAAAGAGAATGAAGAAAAG
1 AAAAAAAGA-AATGAAGAAAAG
48512 AA
1 AA
48514 GCTCTAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 5 0.25
22 7 0.35
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (21 bp):
AAAAAAAGAAATGAAGAAAAG
Found at i:49612 original size:19 final size:19
Alignment explanation
Indices: 49590--49633 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
49580 AAAATCAATT
* *
49590 AAAAAAAGGAAA-AGAAGCA
1 AAAAAAAAGAAAGAAAAG-A
49609 AAAAAAAAGAAAGAAAAGA
1 AAAAAAAAGAAAGAAAAGA
49628 AAAAAA
1 AAAAAA
49634 GTTCAAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAGAAAAGA
Found at i:51739 original size:22 final size:23
Alignment explanation
Indices: 51711--51757 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
51701 CTCCTCCAAT
*
51711 TTTTGCTACAATTTTTCT-TTAG
1 TTTTGCTACAATTTTTATCTTAG
*
51733 TTTTGCTGCAATTTTTATCTTAG
1 TTTTGCTACAATTTTTATCTTAG
51756 TT
1 TT
51758 GAACTGGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.60
Consensus pattern (23 bp):
TTTTGCTACAATTTTTATCTTAG
Found at i:51905 original size:22 final size:22
Alignment explanation
Indices: 51879--51923 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
51869 TTGGGAATTC
51879 TTGATTTAGTTTTCAAAAGAAT
1 TTGATTTAGTTTTCAAAAGAAT
*
51901 TTGATTTAGTTTTCAAGAGAAT
1 TTGATTTAGTTTTCAAAAGAAT
51923 T
1 T
51924 GGTAATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (22 bp):
TTGATTTAGTTTTCAAAAGAAT
Found at i:52807 original size:32 final size:32
Alignment explanation
Indices: 52771--52849 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
52761 CCCAATTATT
* *
52771 AGTTCAGGAGGCAAATTGGTCTAAATTTGCAA
1 AGTTCAGGGGGCAAATTGGCCTAAATTTGCAA
52803 AGTTCAGGGGGCAAATTGGCCTAAATTTGCAA
1 AGTTCAGGGGGCAAATTGGCCTAAATTTGCAA
52835 AGTTCAGGGGGCAAA
1 AGTTCAGGGGGCAAA
52850 AGGGCTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (32 bp):
AGTTCAGGGGGCAAATTGGCCTAAATTTGCAA
Found at i:53014 original size:20 final size:20
Alignment explanation
Indices: 52977--53014 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52967 AGATTAACTT
*
52977 CAAAAAATCCAAAAAAAAGA
1 CAAAAAATCAAAAAAAAAGA
*
52997 CAAAAATTCAAAAAAAAA
1 CAAAAAATCAAAAAAAAA
53015 TATTTTCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.13, G:0.03, T:0.08
Consensus pattern (20 bp):
CAAAAAATCAAAAAAAAAGA
Found at i:53218 original size:19 final size:18
Alignment explanation
Indices: 53194--53237 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
53184 GAAAAATTCG
53194 AAAAAA-AAAAAGGAAAAGT
1 AAAAAACAAAAA--AAAAGT
53213 AAAAAACCAAAAAAAAAGT
1 AAAAAA-CAAAAAAAAAGT
53232 AAAAAA
1 AAAAAA
53238 GATGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 18 0.78
21 5 0.22
ACGTcount: A:0.82, C:0.05, G:0.09, T:0.05
Consensus pattern (18 bp):
AAAAAACAAAAAAAAAGT
Found at i:58798 original size:14 final size:15
Alignment explanation
Indices: 58779--58819 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
58769 AGAATTCATC
58779 ATCTTCATTCTTCA-
1 ATCTTCATTCTTCAG
*
58793 ATCTTCACTCTTCAG
1 ATCTTCATTCTTCAG
58808 ATCTTC-TTCTTC
1 ATCTTCATTCTTC
58820 TTCTCAGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.17, C:0.32, G:0.02, T:0.49
Consensus pattern (15 bp):
ATCTTCATTCTTCAG
Found at i:58831 original size:19 final size:19
Alignment explanation
Indices: 58804--58842 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
58794 TCTTCACTCT
* *
58804 TCAGATCTTCTTCTTCTTC
1 TCAGATCTTCATCATCTTC
*
58823 TCAGTTCTTCATCATCTTC
1 TCAGATCTTCATCATCTTC
58842 T
1 T
58843 TCTTCTTCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.31, G:0.05, T:0.51
Consensus pattern (19 bp):
TCAGATCTTCATCATCTTC
Found at i:58839 original size:28 final size:27
Alignment explanation
Indices: 58773--58852 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
58763 TCTTCAAGAA
*
58773 TTCATCATCTTCATTCTTCAATCTTCACTC
1 TTCATCATCTTC-TTCTTC-TTC-TCACTC
* *
58803 TTCA-GATCTTCTTCTTCTTCTCAGTTC
1 TTCATCATCTTCTTCTTCTTCTCA-CTC
58830 TTCATCATCTTCTTCTTCTTCTC
1 TTCATCATCTTCTTCTTCTTCTC
58853 TTCCTTGTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 3 0.07
27 8 0.18
28 23 0.52
29 6 0.14
30 4 0.09
ACGTcount: A:0.14, C:0.33, G:0.03, T:0.51
Consensus pattern (27 bp):
TTCATCATCTTCTTCTTCTTCTCACTC
Found at i:59681 original size:14 final size:14
Alignment explanation
Indices: 59662--59688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59652 AGCATGGTGG
59662 TTACTAATATAATC
1 TTACTAATATAATC
59676 TTACTAATATAAT
1 TTACTAATATAAT
59689 TTCATTTTTT
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:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
TTACTAATATAATC
Found at i:60172 original size:27 final size:27
Alignment explanation
Indices: 60095--60175 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 27
60085 ATTGTATTGG
*
60095 AATTTTT-A-TTCAATAAATTTTAAATA
1 AATTTTTCATTTC-ATAAATTCTAAATA
** *
60121 AA--TTTCATTAAAATAACATTGTAAATA
1 AATTTTTCATT-TCATAA-ATTCTAAATA
60148 AATTTTTCATTTCATAAATTCTAAATA
1 AATTTTTCATTTCATAAATTCTAAATA
60175 A
1 A
60176 TATAAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
24 3 0.07
25 1 0.02
26 7 0.16
27 21 0.49
28 4 0.09
29 7 0.16
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (27 bp):
AATTTTTCATTTCATAAATTCTAAATA
Found at i:63990 original size:21 final size:23
Alignment explanation
Indices: 63946--63991 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
63936 CTTTGTACAA
63946 ATATAAGGAATATTTAGGTTTTTGG
1 ATATAAGGAATATTT--GTTTTTGG
63971 ATATAAGG-ATATTT-TTTTTGG
1 ATATAAGGAATATTTGTTTTTGG
63992 TTGTTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (23 bp):
ATATAAGGAATATTTGTTTTTGG
Found at i:67743 original size:54 final size:54
Alignment explanation
Indices: 67679--67799 Score: 185
Period size: 54 Copynumber: 2.2 Consensus size: 54
67669 CTACAAAACA
*
67679 AAAAATAGAAAATGAAAATAACTTTTAAAAAATGCAA-GTATC-AA-AAGTTTTCTT
1 AAAAATAGAAAATGAAAA-AAC-TTTAAAAAATG-AACGTACCAAACAAGTTTTCTT
67733 AAAAATAGAAAATGAAAAAACTTTAAAAAATGAACGTACCAAACAAGTTTTCTT
1 AAAAATAGAAAATGAAAAAACTTTAAAAAATGAACGTACCAAACAAGTTTTCTT
67787 AAAAATAGAAAAT
1 AAAAATAGAAAAT
67800 ATAAAATAGA
Statistics
Matches: 63, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
51 2 0.03
52 15 0.24
53 5 0.08
54 41 0.65
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.26
Consensus pattern (54 bp):
AAAAATAGAAAATGAAAAAACTTTAAAAAATGAACGTACCAAACAAGTTTTCTT
Found at i:67807 original size:14 final size:13
Alignment explanation
Indices: 67786--67818 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
67776 CAAGTTTTCT
67786 TAAAAATAGAAAA
1 TAAAAATAGAAAA
67799 TATAAAATAGAAAA
1 TA-AAAATAGAAAA
67813 TAAAAA
1 TAAAAA
67819 CAGTTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (13 bp):
TAAAAATAGAAAA
Found at i:68203 original size:23 final size:23
Alignment explanation
Indices: 68177--68221 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
68167 TTAAATCTAA
*
68177 TATCCTTATACCT-ATTTTATTTT
1 TATCATTATA-CTAATTTTATTTT
*
68200 TATCATTCTACTAATTTTATTT
1 TATCATTATACTAATTTTATTT
68222 AAAAACTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (23 bp):
TATCATTATACTAATTTTATTTT
Done.