Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017809.1 Corchorus olitorius cultivar O-4 contig17842, 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: 67121
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1064 original size:18 final size:17
Alignment explanation
Indices: 1035--1083 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
1025 GTAGTGATCA
1035 TATAACTAATAATAATTGT
1 TATAA-TAATAATAA-TGT
1054 TATAATAATAATAA-GT
1 TATAATAATAATAATGT
*
1070 T-TAATAATTATAAT
1 TATAATAATAATAAT
1084 AAGAAGATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (17 bp):
TATAATAATAATAATGT
Found at i:1192 original size:115 final size:115
Alignment explanation
Indices: 1054--1277 Score: 353
Period size: 115 Copynumber: 1.9 Consensus size: 115
1044 TAATAATTGT
* *
1054 TATAATAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACGTAAAAAAA-TGTTAGTATT
1 TATAATAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACGTAAAAAAATTATTAGTATC
* *
1118 ATTTTAA-ACTTTTGTAATATGGAAAGAAAAACGTAGTGACTAATGATATA
66 A-TTTAAGACTTTTGTAATACGGAAAGAAAAACGTAATGACTAATGATATA
* * *
1168 TATAACTAATAATAATTTTAATAATTATAATAATAAGTTGTTTAACGTAAAAAAATTATTAGTAT
1 TATAA-TAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACGTAAAAAAATTATTAGTAT
1233 CATTTAAGACTTTTGTAATACGGAAAGAAAAACGTAATGACTAAT
65 CATTTAAGACTTTTGTAATACGGAAAGAAAAACGTAATGACTAAT
1278 TCTTCAAAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
114 5 0.05
115 51 0.51
116 44 0.44
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (115 bp):
TATAATAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACGTAAAAAAATTATTAGTATC
ATTTAAGACTTTTGTAATACGGAAAGAAAAACGTAATGACTAATGATATA
Found at i:1315 original size:143 final size:143
Alignment explanation
Indices: 1144--1510 Score: 673
Period size: 142 Copynumber: 2.6 Consensus size: 143
1134 ATATGGAAAG
*
1144 AAAAACGTAGTGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT
1 AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT
1209 TTAACGTAAAAAAATTATTAGTATCATTTAAGACTTTTGTAATACGGAAAGAAAAACGTAATGAC
66 TTAACGTAAAAAAATTATTAGTATCATTTAAGACTTTTGTAATACGGAAAGAAAAACGTAATGAC
*
1274 TAATTCTTCAAAA
131 TAATTCCTCAAAA
1287 AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAAT-ATAAGTTGT
1 AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT
*
1351 TTAACGTAAAAAAATTATTAGTATCATTTAAGACTTTTGTAATATGGAAAGAAAAACGTAATGAC
66 TTAACGTAAAAAAATTATTAGTATCATTTAAGACTTTTGTAATACGGAAAGAAAAACGTAATGAC
1416 TAATTCCTCAAAA
131 TAATTCCTCAAAA
*
1429 AAAAAAGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT
1 AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT
*
1494 TTAATGTAAAAATAATT
66 TTAACGTAAAAA-AATT
1511 GTTATTATTT
Statistics
Matches: 217, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
142 139 0.64
143 74 0.34
144 4 0.02
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.35
Consensus pattern (143 bp):
AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT
TTAACGTAAAAAAATTATTAGTATCATTTAAGACTTTTGTAATACGGAAAGAAAAACGTAATGAC
TAATTCCTCAAAA
Found at i:2411 original size:24 final size:24
Alignment explanation
Indices: 2379--2427 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2369 AGTAATTTTC
2379 ATTTCCTACCCTATTTTTGATATA
1 ATTTCCTACCCTATTTTTGATATA
2403 ATTTCCTACCCTATTTTTGATATA
1 ATTTCCTACCCTATTTTTGATATA
2427 A
1 A
2428 ACACATCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTTCCTACCCTATTTTTGATATA
Found at i:3593 original size:19 final size:20
Alignment explanation
Indices: 3545--3605 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 20
3535 ATCGCTGCTC
3545 TAATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
*
3565 TACATAATCTAATCTGTACAG
1 TA-ATAATCTCATCTGTACAG
*
3586 T-GTAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
3605 T
1 T
3606 TGCCAAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.46
20 2 0.05
21 18 0.49
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
TAATAATCTCATCTGTACAG
Found at i:6883 original size:52 final size:52
Alignment explanation
Indices: 6800--6899 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
6790 AGGTAATTAA
* *
6800 ATCTGACTTATTTATTGCTTTTATTTCAAATTATATATTCTGAAATTGGATT
1 ATCTAACTTATTTATTGCTTTTATTTCAAATTATATACTCTGAAATTGGATT
*
6852 ATCTAACTTATTTATTGCTTTTATTTGAAATTATATACTCTGAAATTG
1 ATCTAACTTATTTATTGCTTTTATTTCAAATTATATACTCTGAAATTG
6900 ATCCTTGCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (52 bp):
ATCTAACTTATTTATTGCTTTTATTTCAAATTATATACTCTGAAATTGGATT
Found at i:10860 original size:5 final size:6
Alignment explanation
Indices: 10827--10859 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
10817 CTTTCGTAAA
10827 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
10860 GTACGCAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:11797 original size:22 final size:22
Alignment explanation
Indices: 11772--11895 Score: 85
Period size: 22 Copynumber: 5.7 Consensus size: 22
11762 TAACAATCAA
11772 ACCAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATAGTGTGGTT
*
11794 ACCAAAGA--TCATA-TAGAGGTT
1 ACCAAA-ATTTCATAGT-GTGGTT
* * *
11815 ATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATAGTGTGGTT
* ** * *
11837 ATCAAAATTTCATACAGAGGTG
1 ACCAAAATTTCATAGTGTGGTT
***
11859 ACCAAAATTTCATAAAAAT-GTT
1 ACCAAAATTTCAT-AGTGTGGTT
11881 ACCAAAATTTCATAG
1 ACCAAAATTTCATAG
11896 GGAGGAAGGT
Statistics
Matches: 80, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.03
21 16 0.20
22 58 0.73
23 4 0.05
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (22 bp):
ACCAAAATTTCATAGTGTGGTT
Found at i:11865 original size:44 final size:43
Alignment explanation
Indices: 11772--11872 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 43
11762 TAACAATCAA
* * *
11772 ACCAAAATTTCATAGTGTGGTTACCAAAGATCATATAGAGGTT
1 ACCAAAATTTCATAGTGTAGTTACCAAAGATCATACAGAGGTG
* * *
11815 ATCAAAACTTCATAGTGTAGTTATCAAA-ATTTCATACAGAGGTG
1 ACCAAAATTTCATAGTGTAGTTACCAAAGA--TCATACAGAGGTG
11859 ACCAAAATTTCATA
1 ACCAAAATTTCATA
11873 AAAATGTTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 24 0.50
44 23 0.48
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (43 bp):
ACCAAAATTTCATAGTGTAGTTACCAAAGATCATACAGAGGTG
Found at i:11972 original size:22 final size:23
Alignment explanation
Indices: 11937--11995 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
11927 AAATTTCCTA
11937 AGAGGTTA-ACAAAAGTTTATAGG
1 AGAGGTTATACAAAAGTTTAT-GG
*
11960 -GAGGTTATA-AAAATTTTATGG
1 AGAGGTTATACAAAAGTTTATGG
* *
11981 AGAGTTTATAGAAAA
1 AGAGGTTATACAAAA
11996 TACATAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 2 0.06
22 24 0.77
23 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.24, T:0.31
Consensus pattern (23 bp):
AGAGGTTATACAAAAGTTTATGG
Found at i:12166 original size:22 final size:22
Alignment explanation
Indices: 12141--12285 Score: 119
Period size: 22 Copynumber: 6.6 Consensus size: 22
12131 TATAGGCAGA
* *
12141 TTATAAAAATTTCACACTGAGG
1 TTATCAAAATTTCACAATGAGG
* * * *
12163 TTATCGAAATTTCATAGTGTGG
1 TTATCAAAATTTCACAATGAGG
*
12185 TTACCAAAATTTCACAATGAGG
1 TTATCAAAATTTCACAATGAGG
* * **
12207 TTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCACAATGAGG
* * *
12229 TTATCGAAATTTTATAATGAGG
1 TTATCAAAATTTCACAATGAGG
* * * *
12251 TTATTAAATTTTCAAAATGTGG
1 TTATCAAAATTTCACAATGAGG
*
12273 TTATCAATATTTC
1 TTATCAAAATTTC
12286 TACATTGCAG
Statistics
Matches: 94, Mismatches: 29, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 94 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCACAATGAGG
Found at i:12220 original size:66 final size:66
Alignment explanation
Indices: 12141--12284 Score: 162
Period size: 66 Copynumber: 2.2 Consensus size: 66
12131 TATAGGCAGA
* * * * * *
12141 TTATAAAAATTTCACACTGAGGTTATCGAAATTTCATAGTGTGGTTACCAAAATTTCACAATGAG
1 TTATCAAATTTTCACACGGAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTTCAAAATGAG
12206 G
66 G
* * * ** * *
12207 TTATCAAATTTTCATAGGGAGGTTATCGAAATTTTATAATGAGGTTATTAAATTTTCAAAATGTG
1 TTATCAAATTTTCACACGGAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTTCAAAATGAG
12272 G
66 G
12273 TTATCAATATTT
1 TTATCAA-ATTT
12285 CTACATTGCA
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
66 60 0.94
67 4 0.06
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (66 bp):
TTATCAAATTTTCACACGGAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTTCAAAATGAG
G
Found at i:12275 original size:44 final size:44
Alignment explanation
Indices: 12141--12285 Score: 166
Period size: 44 Copynumber: 3.3 Consensus size: 44
12131 TATAGGCAGA
* *
12141 TTATAAAAATTTCACACTGAGGTTATCGAAA-TTTCATAGTGTGG
1 TTATCAAAATTTCACAATGAGGTTATC-AAATTTTCATAGTGTGG
* * *
12185 TTACCAAAATTTCACAATGAGGTTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGTGTGG
* * * * * *
12229 TTATCGAAATTTTATAATGAGGTTATTAAATTTTCAAAATGTGG
1 TTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGTGTGG
*
12273 TTATCAATATTTC
1 TTATCAAAATTTC
12286 TACATTGCAG
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
43 3 0.04
44 80 0.96
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (44 bp):
TTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGTGTGG
Found at i:13713 original size:12 final size:12
Alignment explanation
Indices: 13698--13723 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13688 ATTACAAAAC
13698 ATATAACTTAAA
1 ATATAACTTAAA
13710 ATATAACTTAAA
1 ATATAACTTAAA
13722 AT
1 AT
13724 CAGTTTCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATAACTTAAA
Found at i:28867 original size:206 final size:206
Alignment explanation
Indices: 28513--28928 Score: 647
Period size: 206 Copynumber: 2.0 Consensus size: 206
28503 GAACTTGACG
* *
28513 AAAATCTCCTCCAAAAACAATTACTTTTCCTCCAAAATTGTCAGAATTGTTTGTGGTCTCGTAAA
1 AAAATCTCCTCCAAAAACAATTACTTTTCCTCCAAAATTGTCAGAATTGGTTGTGGTCTCATAAA
* * *
28578 CTTCGATCCAAAGTCTCAATTGAAAATCTTTTAGACATTAGAGCTTCATCCCATATGGTAAGCCA
66 CTTCAATCCAAAGTCTCAATTGAAAATCTCTTAGACATTAGAGCTTCATCCCATATGATAAGCCA
* *
28643 TGCTTTTCTTAATAGATGTG-CAGTACCATCTTGTTTTGAATAGTCATATAAAGATGTCTCAGGT
131 TGCTTTTCTTAATAGATGTGTCA-TACCATCTTGTTTTGAATAGCCATATAAAGATGTCTCAGCT
28707 GGGTTTAGTGGC
195 GGGTTTAGTGGC
* *
28719 AAAATCTCCTCCAAAAACAGTTTCTTTTCCTCCAAAAATT-TCAGAATTGGTTGTGGTCTCATAA
1 AAAATCTCCTCCAAAAACAATTACTTTTCCTCC-AAAATTGTCAGAATTGGTTGTGGTCTCATAA
* * * *
28783 ACTTCAATCCAAAGTCTCAATTGAAAATCTCTTAGACATTGGAGTTTCATCCTATATGATAAGTC
65 ACTTCAATCCAAAGTCTCAATTGAAAATCTCTTAGACATTAGAGCTTCATCCCATATGATAAGCC
* * * *
28848 GTGTTTTTCTTAATAGATGTGTTATACCATCTTGTTTTGAATAGCCATATAAAGATGTCTTAGCT
130 ATGCTTTTCTTAATAGATGTGTCATACCATCTTGTTTTGAATAGCCATATAAAGATGTCTCAGCT
28913 GGGTTTAGTGGC
195 GGGTTTAGTGGC
28925 AAAA
1 AAAA
28929 CAAACCTTGA
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
206 184 0.96
207 7 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (206 bp):
AAAATCTCCTCCAAAAACAATTACTTTTCCTCCAAAATTGTCAGAATTGGTTGTGGTCTCATAAA
CTTCAATCCAAAGTCTCAATTGAAAATCTCTTAGACATTAGAGCTTCATCCCATATGATAAGCCA
TGCTTTTCTTAATAGATGTGTCATACCATCTTGTTTTGAATAGCCATATAAAGATGTCTCAGCTG
GGTTTAGTGGC
Found at i:35511 original size:20 final size:20
Alignment explanation
Indices: 35486--35628 Score: 107
Period size: 22 Copynumber: 7.0 Consensus size: 20
35476 GATATTAATA
35486 AGGGGTTATCAAAATTTCAT
1 AGGGGTTATCAAAATTTCAT
*
35506 AGGGGTTATCAAAATTTTAT
1 AGGGGTTATCAAAATTTCAT
*
35526 AGTGTGTTTATCAAAATTTCAT
1 AG-G-GGTTATCAAAATTTCAT
* *
35548 AGTGTAGTTATCAAAATTTTAT
1 AG-G-GGTTATCAAAATTTCAT
* *
35570 -GAGGTTAAT-AAAATTTTAT
1 AGGGGTT-ATCAAAATTTCAT
* *
35589 A--AGTTATCAAAAATCTT-AG
1 AGGGGTTATC-AAAAT-TTCAT
*
35608 AGAGGTTATCAAAATTTCAT
1 AGGGGTTATCAAAATTTCAT
35628 A
1 A
35629 AGTTGATTAT
Statistics
Matches: 101, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.02
18 3 0.03
19 22 0.22
20 32 0.32
21 8 0.08
22 34 0.34
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.39
Consensus pattern (20 bp):
AGGGGTTATCAAAATTTCAT
Found at i:35601 original size:19 final size:18
Alignment explanation
Indices: 35553--35632 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 18
35543 TTCATAGTGT
35553 AGTTATCAAAATTTTATGA
1 AGTTATCAAAATTTTAT-A
*
35572 GGTTAAT-AAAATTTTATA
1 AGTT-ATCAAAATTTTATA
* *
35590 AGTTATCAAAAATCTTAGA
1 AGTTATC-AAAATTTTATA
*
35609 GAGGTTATCAAAATTTCATA
1 -A-GTTATCAAAATTTTATA
35629 AGTT
1 AGTT
35633 GATTATCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
17 2 0.04
18 7 0.14
19 23 0.47
20 11 0.22
21 6 0.12
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (18 bp):
AGTTATCAAAATTTTATA
Found at i:35622 original size:39 final size:37
Alignment explanation
Indices: 35553--35632 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 37
35543 TTCATAGTGT
* * *
35553 AGTTATCAAAATTTTATGAGGTTAATAAAATTTTATA
1 AGTTATCAAAATCTTAAGAGGTTAATAAAATTTCATA
35590 AGTTATCAAAAATCTTAGAGAGGTT-ATCAAAATTTCATA
1 AGTTATC-AAAATCTTA-AGAGGTTAAT-AAAATTTCATA
35629 AGTT
1 AGTT
35633 GATTATCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 7 0.19
38 10 0.27
39 20 0.54
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (37 bp):
AGTTATCAAAATCTTAAGAGGTTAATAAAATTTCATA
Found at i:35768 original size:26 final size:26
Alignment explanation
Indices: 35732--35783 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
35722 CATACTGTTG
* *
35732 TTATTAAAATTTCATGGTATGATTAC
1 TTATGAAAATTTCATAGTATGATTAC
*
35758 TTATGAAAATTTCATAGTGTGATTAC
1 TTATGAAAATTTCATAGTATGATTAC
35784 AAACATTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (26 bp):
TTATGAAAATTTCATAGTATGATTAC
Found at i:35820 original size:22 final size:22
Alignment explanation
Indices: 35687--36153 Score: 272
Period size: 22 Copynumber: 21.0 Consensus size: 22
35677 AAAAAAAGAA
*
35687 GTTATCAAAATTTCAT-TTGAAG
1 GTTATCAAAATTTCATAGTG-AG
* **
35709 GTTATCACAAA-TTCATACTGTT
1 GTTATCA-AAATTTCATAGTGAG
* * *
35731 GTTATTAAAATTTCATGGTATGATTA
1 GTTATCAAAATTTCATAG--TGA--G
* * *
35757 CTTATGAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
* * *
35779 ATTA-CAAACATTCCACAGTGAG
1 GTTATCAAA-ATTTCATAGTGAG
* * *
35801 ATTATCAAAACTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
*
35823 CTTATCAAAATTTCATAG-GAAG
1 GTTATCAAAATTTCATAGTG-AG
35845 GTTATCAAAATTTCATAGTGAG
1 GTTATCAAAATTTCATAGTGAG
35867 GTTATCAAAATTTCATAG-GAAG
1 GTTATCAAAATTTCATAGTG-AG
**
35889 GTTATCAAAATTTCATAGTGCC
1 GTTATCAAAATTTCATAGTGAG
* * * *
35911 GTTATCAAAATTCCACAGGGTG
1 GTTATCAAAATTTCATAGTGAG
*
35933 GTTATCAAAATTTAATAGTGAG
1 GTTATCAAAATTTCATAGTGAG
* * * *
35955 ATTTTCAAAATTTCATTGGGAG
1 GTTATCAAAATTTCATAGTGAG
*
35977 GTT-TACAAAATTTCATTGGTGA-
1 GTTAT-CAAAATTTCA-TAGTGAG
* * * * * * **
35999 ATTCTTGATATTTTCATAATGTC
1 GTT-ATCAAAATTTCATAGTGAG
* *
36022 CTTATCAAAATTTAATAGTTTGA-
1 GTTATCAAAATTTCATAG--TGAG
*
36045 G-TATCAAAATTTCATAGGGAG
1 GTTATCAAAATTTCATAGTGAG
* * *
36066 GTTAACAAAATTTCATTGTGCG
1 GTTATCAAAATTTCATAGTGAG
*
36088 GTT-TCAAAATTTCGTAGTGAG
1 GTTATCAAAATTTCATAGTGAG
* *
36109 G-TATTCTAAATTTCATAATGAG
1 GTTA-TCAAAATTTCATAGTGAG
* * * *
36131 ATTTTCAAGATTTCATAGGGAG
1 GTTATCAAAATTTCATAGTGAG
36153 G
1 G
36154 CTAACAAATT
Statistics
Matches: 338, Mismatches: 82, Indels: 50
0.72 0.17 0.11
Matches are distributed among these distances:
20 3 0.01
21 25 0.07
22 263 0.78
23 25 0.07
24 7 0.02
26 15 0.04
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAG
Found at i:61051 original size:31 final size:31
Alignment explanation
Indices: 61010--61146 Score: 139
Period size: 31 Copynumber: 4.4 Consensus size: 31
61000 TTTGTGCACG
*
61010 TGGCATGCCACGTGTCACTTTTTGAAACACA
1 TGGCATGCCACGTGTCACTTTTTGATACACA
* *
61041 TGGCAAGCCACGTGTCACTTTTTGGTACACA
1 TGGCATGCCACGTGTCACTTTTTGATACACA
* ** * * *
61072 TGACATGATATGTGTCACTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGATACACA
* * * *
61103 TGGCGTGCCACATGTCGCTTTTTGATACACG
1 TGGCATGCCACGTGTCACTTTTTGATACACA
* *
61134 TGACATACCACGT
1 TGGCATGCCACGT
61147 CGGACACCGT
Statistics
Matches: 85, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGATACACA
Found at i:61088 original size:62 final size:62
Alignment explanation
Indices: 61021--61139 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
61011 GGCATGCCAC
* *
61021 GTGTCACTTTTTGAAACACATGGCAAGCCACGTGTCACTTTTTGGTACACATGACATGATAT
1 GTGTCACTTTTTGAAACACATGGCAAGCCACATGTCACTTTTTGATACACATGACATGATAT
** * ** * *
61083 GTGTCACTTTTTGGTACACGTGGCGTGCCACATGTCGCTTTTTGATACACGTGACAT
1 GTGTCACTTTTTGAAACACATGGCAAGCCACATGTCACTTTTTGATACACATGACAT
61140 ACCACGTCGG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 48 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (62 bp):
GTGTCACTTTTTGAAACACATGGCAAGCCACATGTCACTTTTTGATACACATGACATGATAT
Done.