Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021281.1 Corchorus olitorius cultivar O-4 contig21314, 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: 86110
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:42 original size:2 final size:2
Alignment explanation
Indices: 35--73 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25 ATGCAATTTC
35 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
74 AAAGGTTTTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10053 original size:5 final size:5
Alignment explanation
Indices: 10043--10099 Score: 105
Period size: 5 Copynumber: 11.2 Consensus size: 5
10033 TATAAGTTTA
10043 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
10093 AATAAT A
1 -ATAAT A
10100 GTATAGATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 46 0.90
6 5 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:10870 original size:22 final size:22
Alignment explanation
Indices: 10827--10882 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
10817 CCCGAATTTT
*
10827 AATGGTCAAACTACAAATCATG
1 AATGGTCAAACTACAAAGCATG
* **
10849 TATGGTCAAACTGTAAAGCATG
1 AATGGTCAAACTACAAAGCATG
*
10871 AATAGTCAAACT
1 AATGGTCAAACT
10883 CCTTCTAGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (22 bp):
AATGGTCAAACTACAAAGCATG
Found at i:10925 original size:21 final size:23
Alignment explanation
Indices: 10890--10933 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
10880 ACTCCTTCTA
*
10890 GTAATGGGATCAAACCTCAAATC
1 GTAATGGGATCAAACCCCAAATC
10913 GTAAT-GG-TCAAACCCCAAATC
1 GTAATGGGATCAAACCCCAAATC
10934 ATGTATGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 2 0.10
23 5 0.25
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (23 bp):
GTAATGGGATCAAACCCCAAATC
Found at i:10998 original size:87 final size:87
Alignment explanation
Indices: 10811--11068 Score: 329
Period size: 87 Copynumber: 3.0 Consensus size: 87
10801 GCATCCATTG
* ** ** * * *
10811 TGAAACCCCGAATTTTAATGGTCAAACTACAAATCATGTATGGTCAAACTGTAAAGCATGAATAG
1 TGAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAA-TTTAAAGCATGATTAG
* **
10876 TCAAACTCCTT-CTAGTAATGGGA
65 GCAAACT-CTTACTAGTAATAAGA
* *
10899 TCAAACCTCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGG
1 TGAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGG
10964 CAAACTCTTACTAGTAATAAGA
66 CAAACTCTTACTAGTAATAAGA
* *
10986 TGAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATAGTGAAATTTAAAGAATGATTAGG
1 TGAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGG
* * *
11051 AAAACCCCTACTAGTAAT
66 CAAACTCTTACTAGTAAT
11069 GCCCCAAATC
Statistics
Matches: 149, Mismatches: 20, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
86 3 0.02
87 106 0.71
88 40 0.27
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (87 bp):
TGAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGG
CAAACTCTTACTAGTAATAAGA
Found at i:11104 original size:58 final size:58
Alignment explanation
Indices: 11012--11126 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
11002 AATGGTCAAA
*
11012 CCCCAAATCATGTATAGTGAAATTTAAAGAATGATTAGGAAAACCCCTACTAGTAATG
1 CCCCAAATCATGTATAGTGAAATTTAAAGAATGATTAGGAAAACACCTACTAGTAATG
* * * *
11070 CCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGGCAAACACTTACTAGTAAT
1 CCCCAAATCATGTATAGTGAAATTTAAAGAATGATTAGGAAAACACCTACTAGTAAT
11127 AGGATCAAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (58 bp):
CCCCAAATCATGTATAGTGAAATTTAAAGAATGATTAGGAAAACACCTACTAGTAATG
Found at i:11157 original size:21 final size:23
Alignment explanation
Indices: 11122--11165 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
11112 ACACTTACTA
11122 GTAATAGGATCAAACCCCAAATC
1 GTAATAGGATCAAACCCCAAATC
11145 GTAAT-GG-TCAAACCCCAAATC
1 GTAATAGGATCAAACCCCAAATC
11166 ATGTATAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.67
22 2 0.10
23 5 0.24
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.18
Consensus pattern (23 bp):
GTAATAGGATCAAACCCCAAATC
Found at i:11191 original size:145 final size:145
Alignment explanation
Indices: 10925--11214 Score: 535
Period size: 145 Copynumber: 2.0 Consensus size: 145
10915 AATGGTCAAA
* *
10925 CCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGGCAAACTCTTACTAGTAATAAGATGAA
1 CCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGGCAAACACTTACTAGTAATAAGATCAA
10990 ACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATAGTGAAATTTAAAGAATGATTAGGAAAA
66 ACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATAGTGAAATTTAAAGAATGATTAGGAAAA
11055 CCCCTACTAGTAATG
131 CCCCTACTAGTAATG
*
11070 CCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGGCAAACACTTACTAGTAATAGGATCAA
1 CCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGGCAAACACTTACTAGTAATAAGATCAA
* *
11135 ACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATAGTGAAATTTAAAGCATGATTAGGCAAA
66 ACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATAGTGAAATTTAAAGAATGATTAGGAAAA
11200 CCCCTACTAGTAATG
131 CCCCTACTAGTAATG
11215 GGATCAAACC
Statistics
Matches: 140, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 140 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (145 bp):
CCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGGCAAACACTTACTAGTAATAAGATCAA
ACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATAGTGAAATTTAAAGAATGATTAGGAAAA
CCCCTACTAGTAATG
Found at i:11192 original size:87 final size:87
Alignment explanation
Indices: 11070--11301 Score: 376
Period size: 87 Copynumber: 2.7 Consensus size: 87
11060 ACTAGTAATG
* * *
11070 CCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGGCAAACACTTACTAGTAATAGGATCAA
1 CCCCAAATCATGTATAGTGAAATTTAAAGCATGATTAGGCAAACCCCTACTAGTAATAGGATCAA
11135 ACCCCAAA-TCGTAATGGTCAAA
66 ACCCCAAAGT-GTAATGGTCAAA
*
11157 CCCCAAATCATGTATAGTGAAATTTAAAGCATGATTAGGCAAACCCCTACTAGTAATGGGATCAA
1 CCCCAAATCATGTATAGTGAAATTTAAAGCATGATTAGGCAAACCCCTACTAGTAATAGGATCAA
11222 ACCCCAAAGTGTAATGGTCAAA
66 ACCCCAAAGTGTAATGGTCAAA
* * *
11244 CCCCAAATTATGTATTGTGAAACTGTAAAGCATGATTAGGCAAACCCCTACTAGTAAT
1 CCCCAAATCATGTATAGTGAAA-TTTAAAGCATGATTAGGCAAACCCCTACTAGTAAT
11302 GTGGCTAAAT
Statistics
Matches: 136, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
87 101 0.74
88 35 0.26
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (87 bp):
CCCCAAATCATGTATAGTGAAATTTAAAGCATGATTAGGCAAACCCCTACTAGTAATAGGATCAA
ACCCCAAAGTGTAATGGTCAAA
Found at i:11244 original size:21 final size:23
Alignment explanation
Indices: 11209--11250 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
11199 ACCCCTACTA
11209 GTAATGGGATCAAACCCCAAAGT
1 GTAATGGGATCAAACCCCAAAGT
11232 GTAAT-GG-TCAAACCCCAAA
1 GTAATGGGATCAAACCCCAAA
11251 TTATGTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (23 bp):
GTAATGGGATCAAACCCCAAAGT
Found at i:15932 original size:27 final size:27
Alignment explanation
Indices: 15874--15950 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
15864 TAAAAAAATA
**
15874 TTTGCG-TTTTGAAAAAAAAATTTGTT
1 TTTGCGTTTTTGAAAAAAAAATGAGTT
15900 TTTGCGTTTTTGAAAAAAAAA-GAGTT
1 TTTGCGTTTTTGAAAAAAAAATGAGTT
*
15926 TTCTGCGTTTTCTAAAATAAAAAAT
1 TT-TGCGTTTT-TGAAA-AAAAAAT
15951 ATCTTTTCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
26 11 0.26
27 22 0.51
28 4 0.09
29 6 0.14
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (27 bp):
TTTGCGTTTTTGAAAAAAAAATGAGTT
Found at i:19521 original size:20 final size:20
Alignment explanation
Indices: 19484--19522 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19474 CGACTCGAGA
*
19484 AAAATTCGAGTTCGGCTCGG
1 AAAATTCGAGTCCGGCTCGG
19504 AAAATTCGAG-CCGAGCTCG
1 AAAATTCGAGTCCG-GCTCG
19523 AGCCCAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (20 bp):
AAAATTCGAGTCCGGCTCGG
Found at i:19783 original size:28 final size:28
Alignment explanation
Indices: 19743--19807 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
19733 TAGTTAGGGT
* *
19743 TTCCCCTTTTCTTCTTCTTCTCTAGCCG
1 TTCCCCTCTTCTTCTTCTTCTCTACCCG
19771 TTCCCCTCTTCTTCTTCTTCTCTACCCG
1 TTCCCCTCTTCTTCTTCTTCTCTACCCG
19799 TTCCCCTCT
1 TTCCCCTCT
19808 CCACCCTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.03, C:0.45, G:0.05, T:0.48
Consensus pattern (28 bp):
TTCCCCTCTTCTTCTTCTTCTCTACCCG
Found at i:25025 original size:21 final size:21
Alignment explanation
Indices: 24986--25025 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24976 TTAATAGGCA
* *
24986 TTCAAAAACAATTTTATTTAT
1 TTCAAAAACAAATTAATTTAT
*
25007 TTCAAAAATAAATTAATTT
1 TTCAAAAACAAATTAATTT
25026 TAATTTATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (21 bp):
TTCAAAAACAAATTAATTTAT
Found at i:26148 original size:21 final size:22
Alignment explanation
Indices: 26114--26160 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
26104 AAATAAAGAA
*
26114 AAAAAATCTTTTTTTGAGATAAG
1 AAAAAATC-TTTTTTAAGATAAG
*
26137 AAAAAATC-TTTTTAAGATTAG
1 AAAAAATCTTTTTTAAGATAAG
26158 AAA
1 AAA
26161 TAAAGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
23 8 0.36
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (22 bp):
AAAAAATCTTTTTTAAGATAAG
Found at i:28459 original size:31 final size:31
Alignment explanation
Indices: 28416--28487 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
28406 AACAAAACTC
*
28416 GAATGGACCAGTTATGCCGCGACAAGACTGGA
1 GAAT-GACCAGTTATGCAGCGACAAGACTGGA
* *
28448 -ATATGACCAGTTATTCAGTGACAAGACTGGA
1 GA-ATGACCAGTTATGCAGCGACAAGACTGGA
28479 GAATGACCA
1 GAATGACCA
28488 ATTCTGTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (31 bp):
GAATGACCAGTTATGCAGCGACAAGACTGGA
Found at i:31822 original size:43 final size:43
Alignment explanation
Indices: 31761--31849 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
31751 TAGAGAAGTG
31761 CTTCATACAGTTTACCATGACACAATGCAATATATTGTTCTTT
1 CTTCATACAGTTTACCATGACACAATGCAATATATTGTTCTTT
*
31804 CTTCATACAGTTTACCATGACACGATGCAATATATTGTTCTTT
1 CTTCATACAGTTTACCATGACACAATGCAATATATTGTTCTTT
31847 CTT
1 CTT
31850 TGGTACTTAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.40
Consensus pattern (43 bp):
CTTCATACAGTTTACCATGACACAATGCAATATATTGTTCTTT
Found at i:35389 original size:12 final size:13
Alignment explanation
Indices: 35372--35404 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
35362 TAGAAGGAAA
35372 AGAAATCAG-TGT
1 AGAAATCAGATGT
35384 AGAAATC-GATGT
1 AGAAATCAGATGT
35396 AGAAATCAG
1 AGAAATCAG
35405 GAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.21
Consensus pattern (13 bp):
AGAAATCAGATGT
Found at i:41526 original size:74 final size:76
Alignment explanation
Indices: 41418--41571 Score: 276
Period size: 74 Copynumber: 2.0 Consensus size: 76
41408 TTTGAATGGT
41418 TTGGCTAAATTTCTGAGTTAATAGATAGAATAGAACTGAAGAGATATCATAGTTCAAATGAAGAT
1 TTGGCTAAATTTCT-AG-TAATAGATAGAATAGAACTGAAGAGATATCATAGTTCAAATGAAGAT
41483 TTCTGAAGAAATG
64 TTCTGAAGAAATG
41496 TTGGCTAAATTTCT-G-AATAGATAGAATAGAACTGAAGAGATATCATAGTTCAAATGAAGATTT
1 TTGGCTAAATTTCTAGTAATAGATAGAATAGAACTGAAGAGATATCATAGTTCAAATGAAGATTT
41559 CTGAAGAAATG
66 CTGAAGAAATG
41570 TT
1 TT
41572 TCCACAGAGC
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
74 61 0.80
76 1 0.01
78 14 0.18
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (76 bp):
TTGGCTAAATTTCTAGTAATAGATAGAATAGAACTGAAGAGATATCATAGTTCAAATGAAGATTT
CTGAAGAAATG
Found at i:45014 original size:22 final size:22
Alignment explanation
Indices: 44989--45034 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
44979 GAATTGTCAA
44989 TTCAAATGCAGGGACTAACTGT
1 TTCAAATGCAGGGACTAACTGT
45011 TTCAAATGCAGGGACTAACTGT
1 TTCAAATGCAGGGACTAACTGT
45033 TT
1 TT
45035 GCTCCACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (22 bp):
TTCAAATGCAGGGACTAACTGT
Found at i:46555 original size:40 final size:40
Alignment explanation
Indices: 46510--46590 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
46500 TGCTGATATC
46510 AGAATCCCACTCTTGTCACTTTGCCACCTGAAGATTTCAT
1 AGAATCCCACTCTTGTCACTTTGCCACCTGAAGATTTCAT
46550 AGAATCCCACTCTTGTCACTTTGCCACCTGAAGATTTCAT
1 AGAATCCCACTCTTGTCACTTTGCCACCTGAAGATTTCAT
46590 A
1 A
46591 CATAGCAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (40 bp):
AGAATCCCACTCTTGTCACTTTGCCACCTGAAGATTTCAT
Found at i:59749 original size:30 final size:30
Alignment explanation
Indices: 59687--59771 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
59677 GTTCTTTTTT
* ** *
59687 TTTAATTGCTGCTATTTGGGGGCTGGTTGTG
1 TTTAATTGCTGCAATTT-GGGGCTTATGGTG
*
59718 TTTGATTGCTGCAATTTGGGGCTTATGGTG
1 TTTAATTGCTGCAATTTGGGGCTTATGGTG
*
59748 TTTAATTGCTGCAATTTGAGGCTT
1 TTTAATTGCTGCAATTTGGGGCTT
59772 GATTGTATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 32 0.68
31 15 0.32
ACGTcount: A:0.14, C:0.11, G:0.31, T:0.45
Consensus pattern (30 bp):
TTTAATTGCTGCAATTTGGGGCTTATGGTG
Found at i:61556 original size:19 final size:18
Alignment explanation
Indices: 61532--61567 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
61522 TGAAGACCAT
61532 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
61551 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
61568 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:63387 original size:21 final size:21
Alignment explanation
Indices: 63346--63387 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
63336 GGTAATCAAG
* *
63346 AGTTTTTAAGATTTAAACAGA
1 AGTTTTCAAGATTCAAACAGA
63367 AGTTTTCAA-ATTCAAATCAGA
1 AGTTTTCAAGATTCAAA-CAGA
63388 CTTAGTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (21 bp):
AGTTTTCAAGATTCAAACAGA
Found at i:72649 original size:19 final size:20
Alignment explanation
Indices: 72616--72653 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
72606 AATTATTTCG
72616 TTTGGGCTTACTTTATTTGT
1 TTTGGGCTTACTTTATTTGT
*
72636 TTTGGG-TTAGTTTATTTG
1 TTTGGGCTTACTTTATTTG
72654 GGCTTGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.11, C:0.05, G:0.24, T:0.61
Consensus pattern (20 bp):
TTTGGGCTTACTTTATTTGT
Found at i:76438 original size:55 final size:54
Alignment explanation
Indices: 76348--76458 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 54
76338 TACGCCGCGG
*
76348 GTCTTTTTATTCTCTGGAATTAAGTTATTAATTTATTTTAAGATTTTAATCTTGT
1 GTCTTTTTATTCTCCGGAATTAAGTTATTAATTTA-TTTAAGATTTTAATCTTGT
* *
76403 GTCTTTTTATTCTCCGGAATTAAGTTGTTAGTTTATTTAAGATTTTAATCTTGT
1 GTCTTTTTATTCTCCGGAATTAAGTTATTAATTTATTTAAGATTTTAATCTTGT
76457 GT
1 GT
76459 AAGAAAGAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 21 0.40
55 32 0.60
ACGTcount: A:0.23, C:0.08, G:0.14, T:0.55
Consensus pattern (54 bp):
GTCTTTTTATTCTCCGGAATTAAGTTATTAATTTATTTAAGATTTTAATCTTGT
Found at i:76656 original size:19 final size:20
Alignment explanation
Indices: 76618--76656 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
76608 AACAAAATAG
*
76618 AAAAATATTAGGGTCTATTT
1 AAAAAAATTAGGGTCTATTT
76638 AAAAAAATTAGGGTC-ATTT
1 AAAAAAATTAGGGTCTATTT
76657 GATAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (20 bp):
AAAAAAATTAGGGTCTATTT
Found at i:76947 original size:17 final size:18
Alignment explanation
Indices: 76914--76950 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
76904 GGGGCACTAT
76914 TTCACTAAAAGCCCATTA
1 TTCACTAAAAGCCCATTA
*
76932 TTCATTAAAA-CCCATTA
1 TTCACTAAAAGCCCATTA
76949 TT
1 TT
76951 TACTTATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (18 bp):
TTCACTAAAAGCCCATTA
Found at i:77253 original size:20 final size:20
Alignment explanation
Indices: 77228--77267 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
77218 AATTACAAAC
77228 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
77248 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
77268 TTGAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:78027 original size:52 final size:52
Alignment explanation
Indices: 77963--78321 Score: 583
Period size: 52 Copynumber: 6.9 Consensus size: 52
77953 GGGATCTTTC
* * * *
77963 CCTAAATCGAACATTTTGAAAACTTGGTGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* *
78015 GCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* *
78067 CCTAAATCGAATGCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* *
78119 CCTAAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCACTTTGAAGAGA
1 CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
*
78171 GCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* * * *
78223 GCTAAATTGAACACTTTGGAAACCTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
78275 CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGA
1 CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGA
78322 GAACTTTGAA
Statistics
Matches: 285, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 285 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
Found at i:84659 original size:27 final size:27
Alignment explanation
Indices: 84621--84676 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
84611 TGAAAGGCAA
84621 CTATCAAGCACCAATTAATATATGAGC
1 CTATCAAGCACCAATTAATATATGAGC
*
84648 CTATCAAGCACCGATTAATATATGAGC
1 CTATCAAGCACCAATTAATATATGAGC
84675 CT
1 CT
84677 GAGAAGGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (27 bp):
CTATCAAGCACCAATTAATATATGAGC
Done.