Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024074.1 Corchorus olitorius cultivar O-4 contig24107, 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: 88415
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:63 original size:31 final size:31
Alignment explanation
Indices: 2--86 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
1 T
* *
2 CTTATATTTTTCTTTTGGGAC-AGAAAATCC
1 CTTATGTTTTTCTTTTGGGACAAAAAAATCC
32 CTTATGTTTTTCTTTTGGGACAAAAAAATCC
1 CTTATGTTTTTCTTTTGGGACAAAAAAATCC
63 CTTATGTTTTTCTTTTGGGACAAA
1 CTTATGTTTTTCTTTTGGGACAAA
87 TCAGTCCCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
30 20 0.38
31 32 0.62
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (31 bp):
CTTATGTTTTTCTTTTGGGACAAAAAAATCC
Found at i:241 original size:29 final size:30
Alignment explanation
Indices: 199--272 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 30
189 CTCATTTTTG
* *
199 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
228 AAACATAAGGGATTAATTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
259 AAACATAAGGGATT
1 AAACATAAGGGATT
273 TTTTTGGGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 26 0.63
31 15 0.37
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.23
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:1542 original size:16 final size:15
Alignment explanation
Indices: 1521--1560 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1511 TTACTTTGCT
1521 TTGTTTTCTAGTATAA
1 TTGTTTTCT-GTATAA
*
1537 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTATAA
*
1552 TTGCTTTCT
1 TTGTTTTCT
1561 TTCAACTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (15 bp):
TTGTTTTCTGTATAA
Found at i:1554 original size:15 final size:15
Alignment explanation
Indices: 1521--1578 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
1511 TTACTTTGCT
*
1521 TTGTTTTCTAGTATAA
1 TTGTTTTCT-GTTTAA
1537 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
* *
1552 TTGCTTTCT-TTCAA
1 TTGTTTTCTGTTTAA
1566 CTCTGTTTTCTGT
1 -T-TGTTTTCTGT
1579 GTTTTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 4 0.11
15 14 0.40
16 16 0.46
17 1 0.03
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:7909 original size:13 final size:13
Alignment explanation
Indices: 7888--7919 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
7878 ACTACTAATA
7888 TTTTCTTTTGAGT
1 TTTTCTTTTGAGT
*
7901 TTTTTTTTTGAGT
1 TTTTCTTTTGAGT
7914 TTTTCT
1 TTTTCT
7920 AGGAAGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.75
Consensus pattern (13 bp):
TTTTCTTTTGAGT
Found at i:10513 original size:10 final size:10
Alignment explanation
Indices: 10498--10523 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
10488 AATTAACAAG
10498 ATAATTAGAA
1 ATAATTAGAA
10508 ATAATTAGAA
1 ATAATTAGAA
10518 ATAATT
1 ATAATT
10524 TCTGAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (10 bp):
ATAATTAGAA
Found at i:14612 original size:11 final size:11
Alignment explanation
Indices: 14572--14625 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
14562 TTGCTCCTTG
14572 AAATAATTCTTC
1 AAATAA-TCTTC
*
14584 -AATGATCTTC
1 AAATAATCTTC
14594 --AT-ATCTTC
1 AAATAATCTTC
14602 AAATAATCTTC
1 AAATAATCTTC
*
14613 AATTAATCTTC
1 AAATAATCTTC
14624 AA
1 AA
14626 TCACGAACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 6 0.16
9 2 0.05
10 7 0.19
11 22 0.59
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.41
Consensus pattern (11 bp):
AAATAATCTTC
Found at i:17865 original size:15 final size:15
Alignment explanation
Indices: 17845--17876 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17835 TTCAAGTTAG
*
17845 AAATTAAAAATTTAA
1 AAATTAAAAATTGAA
17860 AAATTAAAAATTGAA
1 AAATTAAAAATTGAA
17875 AA
1 AA
17877 TAAGTAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAATTAAAAATTGAA
Found at i:18167 original size:30 final size:30
Alignment explanation
Indices: 18131--18187 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
18121 CTTCACAAGG
18131 TCCATGCCATCTCGATCTGTCATGTATAGC
1 TCCATGCCATCTCGATCTGTCATGTATAGC
18161 TCCATGCCATCTCGATCTGTCATGTAT
1 TCCATGCCATCTCGATCTGTCATGTAT
18188 GGCTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (30 bp):
TCCATGCCATCTCGATCTGTCATGTATAGC
Found at i:18642 original size:25 final size:25
Alignment explanation
Indices: 18593--18642 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
18583 ATGATTGCAC
**
18593 AATCTTGTTGCAAAAGTGAGTTCCT
1 AATCTTGTTGCAAAAGTGAACTCCT
18618 AATCTTGTTGCAAAAGTGAACTCCT
1 AATCTTGTTGCAAAAGTGAACTCCT
18643 TGATTGGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (25 bp):
AATCTTGTTGCAAAAGTGAACTCCT
Found at i:22929 original size:15 final size:15
Alignment explanation
Indices: 22909--22953 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
22899 TAAAAGTTCT
22909 TAAAAATAAAAAAAA
1 TAAAAATAAAAAAAA
*
22924 TAAAAAATAAAAAACA
1 T-AAAAATAAAAAAAA
*
22940 GAAAAATAAGAAAA
1 TAAAAATAA-AAAA
22954 TCTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.11
Consensus pattern (15 bp):
TAAAAATAAAAAAAA
Found at i:23006 original size:34 final size:32
Alignment explanation
Indices: 22967--23045 Score: 79
Period size: 34 Copynumber: 2.3 Consensus size: 32
22957 TTTTTTTTTC
22967 AAAACGCAAAACCAAAAATTTTTCTTTT-AAATTA
1 AAAACGCAAAA-C--AAATTTTTCTTTTAAAATTA
* *
23001 AAAACGCGGAAACAAATTTTTTTTTTAGAAATTA
1 AAAACGC-AAAACAAATTTTTCTTTTA-AAATTA
*
23035 AAAACACAAAA
1 AAAACGCAAAA
23046 GTCAAGGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 12 0.32
33 3 0.08
34 20 0.53
35 3 0.08
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (32 bp):
AAAACGCAAAACAAATTTTTCTTTTAAAATTA
Found at i:28600 original size:19 final size:18
Alignment explanation
Indices: 28576--28611 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28566 TGAAGACCAT
28576 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
28595 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
28612 TTTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:29215 original size:11 final size:11
Alignment explanation
Indices: 29199--29224 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29189 AGATAATTTC
29199 TTTTCTTCTAG
1 TTTTCTTCTAG
29210 TTTTCTTCTAG
1 TTTTCTTCTAG
29221 TTTT
1 TTTT
29225 TTAGGCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:31288 original size:41 final size:43
Alignment explanation
Indices: 31207--31292 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 43
31197 TGTTTTTCTT
* **
31207 TTATTTTCTTCTTTCCGTTCTTTGCGTTTTTAATTTAAAAAAA
1 TTATTTTCTTCTTTCCGTTCATTGCGTTTTTAATAAAAAAAAA
*
31250 TTATTTT-TTCTTTTC-TTCATTGCGTTTTTGAA-AAAAAAAAA
1 TTATTTTCTTCTTTCCGTTCATTGCGTTTTT-AATAAAAAAAAA
31291 TT
1 TT
31293 GGCGATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 22 0.58
42 9 0.24
43 7 0.18
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.55
Consensus pattern (43 bp):
TTATTTTCTTCTTTCCGTTCATTGCGTTTTTAATAAAAAAAAA
Found at i:34554 original size:19 final size:18
Alignment explanation
Indices: 34530--34565 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34520 TGAATACCAT
34530 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
34549 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
34566 TTTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:35169 original size:11 final size:11
Alignment explanation
Indices: 35153--35178 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35143 AGATAATTCC
35153 TTTTCTTCTAG
1 TTTTCTTCTAG
35164 TTTTCTTCTAG
1 TTTTCTTCTAG
35175 TTTT
1 TTTT
35179 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:41572 original size:27 final size:27
Alignment explanation
Indices: 41542--41637 Score: 92
Period size: 23 Copynumber: 3.7 Consensus size: 27
41532 GGGCATCCAA
* *
41542 GGGCATTTTGGTCATTTGCATGTTCAG
1 GGGCATTTTGGTCATTTGCATATTTAG
* *
41569 GGGCATTTTGGTC-TTT---TTTTTAA
1 GGGCATTTTGGTCATTTGCATATTTAG
* *
41592 GGGCATTTTGGTCATTCGCACATTTAGG
1 GGGCATTTTGGTCATTTGCATATTTA-G
*
41620 GGGCATTTTGGTCTTTTG
1 GGGCATTTTGGTCATTTG
41638 ATCCATTTAG
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
23 17 0.31
24 2 0.04
26 3 0.05
27 17 0.31
28 16 0.29
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTGCATATTTAG
Found at i:41598 original size:50 final size:51
Alignment explanation
Indices: 41540--41636 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 51
41530 AGGGGCATCC
* **
41540 AAGGGCATTTTGGTCATTTGCATGTTCA-GGGGCATTTTGGTCTTTTTTTT
1 AAGGGCATTTTGGTCATTCGCACATTCAGGGGGCATTTTGGTCTTTTTTTT
*
41590 AAGGGCATTTTGGTCATTCGCACATTTAGGGGGCATTTTGGTCTTTT
1 AAGGGCATTTTGGTCATTCGCACATTCAGGGGGCATTTTGGTCTTTT
41637 GATCCATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 24 0.57
51 18 0.43
ACGTcount: A:0.15, C:0.13, G:0.27, T:0.44
Consensus pattern (51 bp):
AAGGGCATTTTGGTCATTCGCACATTCAGGGGGCATTTTGGTCTTTTTTTT
Found at i:43311 original size:60 final size:60
Alignment explanation
Indices: 43218--43338 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
43208 CTCACACTCG
* *
43218 ACAGACTCCGCTTTTTCTCTCTTCCATTGAAACACTCAAGCTCATCCATACCATATACAC
1 ACAGACTACACTTTTTCTCTCTTCCATTGAAACACTCAAGCTCATCCATACCATATACAC
*
43278 ACAGACTACACTTTTTCTTTCTTCCATTGAAACACTCAAGCTCATCCATACCATATACAC
1 ACAGACTACACTTTTTCTCTCTTCCATTGAAACACTCAAGCTCATCCATACCATATACAC
43338 A
1 A
43339 AAAAAAATGG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.31
Consensus pattern (60 bp):
ACAGACTACACTTTTTCTCTCTTCCATTGAAACACTCAAGCTCATCCATACCATATACAC
Found at i:43360 original size:60 final size:59
Alignment explanation
Indices: 43226--43360 Score: 180
Period size: 60 Copynumber: 2.2 Consensus size: 59
43216 CGACAGACTC
* * **
43226 CGCTTTTTCTCTCTTCCATTGAAACACTCAAGCTCATCCATACCATATACACACAGACTA
1 CGCTTTTTCT-TCTTCCATTGAAACACTCAAGCTCATCCATACCATATACACAAAAAAAA
*
43286 CACTTTTTCTTTCTTCCATTGAAACACTCAAGCTCATCCATACCATATACACAAAAAAAA
1 CGCTTTTTC-TTCTTCCATTGAAACACTCAAGCTCATCCATACCATATACACAAAAAAAA
* *
43346 TGGCTTCTTCTTCTT
1 -CGCTTTTTCTTCTT
43361 AAAAAAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
60 58 0.89
61 7 0.11
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (59 bp):
CGCTTTTTCTTCTTCCATTGAAACACTCAAGCTCATCCATACCATATACACAAAAAAAA
Found at i:44132 original size:41 final size:40
Alignment explanation
Indices: 44030--44132 Score: 98
Period size: 41 Copynumber: 2.5 Consensus size: 40
44020 TCTTTTGGGT
* * * * *
44030 CCCTGATTTAGTGTTTCATTTGTTAATTGATTCGATTTTGT
1 CCCTGATTTAG-GTTTTATTTATTAATTGATTCAATTTCGC
* ** *
44071 CCCTAATTTAAGGTAATATTTATTTATTGATTCAATTTCGC
1 CCCTGATTT-AGGTTTTATTTATTAATTGATTCAATTTCGC
44112 CCCTGATTTAGGATTTTATTT
1 CCCTGATTTAGG-TTTTATTT
44133 TTGATTTATG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
40 3 0.06
41 43 0.90
42 2 0.04
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (40 bp):
CCCTGATTTAGGTTTTATTTATTAATTGATTCAATTTCGC
Found at i:44807 original size:7 final size:8
Alignment explanation
Indices: 44779--44823 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
44769 ATTTGAAGGA
44779 AAAAAATG
1 AAAAAATG
44787 AAAAAA-G
1 AAAAAATG
44794 AAGAAAA-G
1 AA-AAAATG
44802 AAAAAATG
1 AAAAAATG
44810 -AAAAATG
1 AAAAAATG
*
44817 GAAAAAT
1 AAAAAAT
44824 CAGAAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.41
8 20 0.59
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:44830 original size:16 final size:16
Alignment explanation
Indices: 44781--44836 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
44771 TTGAAGGAAA
*
44781 AAAATGAAAAAAGAAG
1 AAAATGAAAAAATAAG
*
44797 AAAA-GAAAAAATGA-
1 AAAATGAAAAAATAAG
* *
44811 AAAATGGAAAAATCAG
1 AAAATGAAAAAATAAG
*
44827 AAAATTAAAA
1 AAAATGAAAA
44837 GATGTAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 4 0.12
15 16 0.50
16 12 0.38
ACGTcount: A:0.73, C:0.02, G:0.14, T:0.11
Consensus pattern (16 bp):
AAAATGAAAAAATAAG
Found at i:46351 original size:20 final size:20
Alignment explanation
Indices: 46326--46363 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
46316 TACATACTGC
46326 AATAATTAAACAACTAAGGT
1 AATAATTAAACAACTAAGGT
46346 AATAATTAAACAACTAAG
1 AATAATTAAACAACTAAG
46364 ACCTGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAATTAAACAACTAAGGT
Found at i:47599 original size:45 final size:45
Alignment explanation
Indices: 47502--47599 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
47492 CAGCTTCAAG
* *
47502 CCGATGGAGTAATTGCCCCTTACCATCGGTATTCACTTCCTTATC
1 CCGATGGTGTAATTGCCCCTTACCATCGGTACTCACTTCCTTATC
** *
47547 CCGATGGTGTAATTGCTTCTTACCATCGGTACTCACTTCCTTGTC
1 CCGATGGTGTAATTGCCCCTTACCATCGGTACTCACTTCCTTATC
*
47592 CGGATGGT
1 CCGATGGT
47600 ATTAACATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (45 bp):
CCGATGGTGTAATTGCCCCTTACCATCGGTACTCACTTCCTTATC
Found at i:49269 original size:42 final size:43
Alignment explanation
Indices: 49218--49305 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 43
49208 TGCATTACCT
* *
49218 AAATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTA
1 AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
49260 AAATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTA
1 AAATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTA
49305 A
1 A
49306 TATTAATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 8 0.20
45 33 0.80
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.31
Consensus pattern (43 bp):
AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
Found at i:50773 original size:2 final size:2
Alignment explanation
Indices: 50730--50754 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50720 TACTATTTAG
50730 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
50755 TCACTAAAAA
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:61256 original size:2 final size:2
Alignment explanation
Indices: 61249--61287 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
61239 TTTGGCCATG
61249 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
61288 TGAAATTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66631 original size:68 final size:67
Alignment explanation
Indices: 66446--66641 Score: 230
Period size: 68 Copynumber: 2.9 Consensus size: 67
66436 CTAAATTCGT
** * * *
66446 TTTTCTTTCCTCTTAAGTATTAATCAAACCTATTGACAACGACGGAAATAATAGTTGCCTCAAAT
1 TTTTCTTGACTCTTAAGTATTAATAAAACCTATTAACAACGAC-GAAATGATAGTTGCCTCAAAT
66511 TTG
65 TTG
* * ** **
66514 TTTTCTTGACGCTTAAGTATCAATAAAATTTATTAAGGACGACTGAAATGATAGTTGCCTCAAAT
1 TTTTCTTGACTCTTAAGTATTAATAAAACCTATTAACAACGAC-GAAATGATAGTTGCCTCAAAT
66579 TTG
65 TTG
** * *
66582 TTTTCTTGACTCTTAAGTATTAATAAAACCTATCCACAACTACGAAAATGATAATTGCCT
1 TTTTCTTGACTCTTAAGTATTAATAAAACCTATTAACAACGACG-AAATGATAGTTGCCT
66642 TTTTTTTAAT
Statistics
Matches: 105, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
67 1 0.01
68 104 0.99
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (67 bp):
TTTTCTTGACTCTTAAGTATTAATAAAACCTATTAACAACGACGAAATGATAGTTGCCTCAAATT
TG
Found at i:69070 original size:108 final size:108
Alignment explanation
Indices: 68881--69201 Score: 597
Period size: 108 Copynumber: 3.0 Consensus size: 108
68871 TAGTAAGAGG
*
68881 GATTGTTCTAATTATTGGAGGAATAAAGATCCTCTATTTGCATATAGAACTAAGCTTCGCATCTT
1 GATTGTTCTAATTATTGGAGGAATAAAGATCCTCTATTTGCATATAGAACTAAGCTTCGTATCTT
*
68946 AATCGTCGGTTAGACTTAACTGCTCTGCTGTTGTGGAAAACAT
66 AATCGTCGGTTAGACTTAACTGTTCTGCTGTTGTGGAAAACAT
68989 GATTGTTCTAATTATTGGAGGAATAAAGATCCTCTATTTGCATATAGAACTAAGCTTCGTATCTT
1 GATTGTTCTAATTATTGGAGGAATAAAGATCCTCTATTTGCATATAGAACTAAGCTTCGTATCTT
*
69054 AATCGTTGGTTAGACTTAACTGTTCTGCTGTTGTGGAAAACAT
66 AATCGTCGGTTAGACTTAACTGTTCTGCTGTTGTGGAAAACAT
*
69097 GATTGTGCTAATTATTGGAGGAATAAAGATCCTCTATTTGCATATAGAACTAAGCTTCGTATCTT
1 GATTGTTCTAATTATTGGAGGAATAAAGATCCTCTATTTGCATATAGAACTAAGCTTCGTATCTT
*
69162 AATCGTCGGTTAGACTTAACTGTTCTGCCGTTGTGGAAAA
66 AATCGTCGGTTAGACTTAACTGTTCTGCTGTTGTGGAAAA
69202 TGTTTGTTGG
Statistics
Matches: 207, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 207 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (108 bp):
GATTGTTCTAATTATTGGAGGAATAAAGATCCTCTATTTGCATATAGAACTAAGCTTCGTATCTT
AATCGTCGGTTAGACTTAACTGTTCTGCTGTTGTGGAAAACAT
Found at i:75729 original size:76 final size:77
Alignment explanation
Indices: 75639--75792 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 77
75629 AATAGTCAGA
75639 ATCAGAATAAAAGGTTCTTTCTTTATATGTGTCTTCTATCATA-CTTGCATATAATTGTTTTGGC
1 ATCAGAATAAAAGGTTCTTTCTTTATATGTGTCTTCTATCATATCTTGCATATAATTGTTTTGGC
75703 CATATCTTCTTT
66 CATATCTTCTTT
*
75715 ATCAGAATCAAAGGTTCTTTCTTTATATGTGTCTTCTATCATACTTCTTGCATATAATTGTTTTG
1 ATCAGAATAAAAGGTTCTTTCTTTATATGTGTCTTCTATCATA--TCTTGCATATAATTGTTTTG
75780 GCCATATCTTCTT
64 GCCATATCTTCTT
75793 CATGCAGTTT
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
76 42 0.57
79 32 0.43
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (77 bp):
ATCAGAATAAAAGGTTCTTTCTTTATATGTGTCTTCTATCATATCTTGCATATAATTGTTTTGGC
CATATCTTCTTT
Found at i:80570 original size:31 final size:33
Alignment explanation
Indices: 80530--80616 Score: 110
Period size: 31 Copynumber: 2.8 Consensus size: 33
80520 ACATGCTATG
* *
80530 TGTACCAAAAAGCGACACGTGGCATAC-T-ACA
1 TGTATCAAAAAGTGACACGTGGCATACGTCACA
*
80561 TGTATCAAAAAGTGACATGTGGC--ACGTCACA
1 TGTATCAAAAAGTGACACGTGGCATACGTCACA
*
80592 TGTATCAAAAAATGACACGTGGCAT
1 TGTATCAAAAAGTGACACGTGGCAT
80617 GCCTCGTGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 2 0.04
30 1 0.02
31 44 0.94
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (33 bp):
TGTATCAAAAAGTGACACGTGGCATACGTCACA
Found at i:84664 original size:17 final size:16
Alignment explanation
Indices: 84639--84699 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
84629 AGTAGTTAGA
* *
84639 AATATTAAATTAGAAT
1 AATAATAAATTAAAAT
84655 AATAATTAAATTTAACAAT
1 AATAA-TAAA-TTAA-AAT
84674 --TAATAAATTAAAAT
1 AATAATAAATTAAAAT
84688 AATAATAAATTA
1 AATAATAAATTA
84700 CAAAATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.08
15 4 0.11
16 18 0.47
17 7 0.18
18 3 0.08
19 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
AATAATAAATTAAAAT
Found at i:85089 original size:20 final size:19
Alignment explanation
Indices: 85060--85098 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
85050 AAAGGATAGC
*
85060 AAATAGTAACAAATAAAAAG
1 AAATACTAACAAA-AAAAAG
85080 AAATACTAACAAAAAAAAG
1 AAATACTAACAAAAAAAAG
85099 GACACGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.13
Consensus pattern (19 bp):
AAATACTAACAAAAAAAAG
Found at i:87553 original size:21 final size:22
Alignment explanation
Indices: 87529--87571 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
87519 AAAAGTCAAC
*
87529 AAACCGAATCCG-CCCAACCCA
1 AAACCGAAACCGACCCAACCCA
*
87550 AAACCGAAACTGACCCAACCCA
1 AAACCGAAACCGACCCAACCCA
87572 GAAATGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.42, C:0.44, G:0.09, T:0.05
Consensus pattern (22 bp):
AAACCGAAACCGACCCAACCCA
Found at i:87618 original size:16 final size:16
Alignment explanation
Indices: 87594--87634 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
87584 ATTTTTGGGT
*
87594 ACCCGAACCCGAAATG
1 ACCCGAACCCAAAATG
*
87610 ACCCCAACCCAAAATG
1 ACCCGAACCCAAAATG
87626 ACCCGAACC
1 ACCCGAACC
87635 TGATCAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.44, G:0.12, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCAAAATG
Found at i:88317 original size:2 final size:2
Alignment explanation
Indices: 88305--88346 Score: 66
Period size: 2 Copynumber: 20.0 Consensus size: 2
88295 GAAAGTCTAT
88305 TA TA GTA TA TA TA TA CTA 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 TA TA TA TA
88347 GAGAGAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 34 0.89
3 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:88351 original size:2 final size:2
Alignment explanation
Indices: 88346--88415 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
88336 ATATATATAT
88346 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
88388 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.