Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024871.1 Corchorus olitorius cultivar O-4 contig24904, 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: 181923
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2248 original size:14 final size:14
Alignment explanation
Indices: 2229--2258 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2219 TTTATTATTA
*
2229 TTCTTCTTCTTTTC
1 TTCTTCTTCTTCTC
2243 TTCTTCTTCTTCTC
1 TTCTTCTTCTTCTC
2257 TT
1 TT
2259 GCTCCTGCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTTCTTCTTCTC
Found at i:9346 original size:2 final size:2
Alignment explanation
Indices: 9339--9384 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
9329 TTAGAAGTGA
* *
9339 AT AT AT AT TT AT AT TT AT -T AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9379 AT AT AT
1 AT AT AT
9385 TTAAAGATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:30283 original size:29 final size:29
Alignment explanation
Indices: 30241--30296 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
30231 TCATCGGATC
*
30241 GTGTAGCTCTGGGCTCTAACTTGTGAATT
1 GTGTAGCCCTGGGCTCTAACTTGTGAATT
*
30270 GTGTAGCCCTGGGCTCTGACTTGTGAA
1 GTGTAGCCCTGGGCTCTAACTTGTGAA
30297 GCATCACGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (29 bp):
GTGTAGCCCTGGGCTCTAACTTGTGAATT
Found at i:43704 original size:45 final size:45
Alignment explanation
Indices: 43640--43726 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
43630 ACTAAATCTA
*
43640 ATGGTTTCAACTCAATTGCCAAGCTGCCCTCACTCGCCGCTTGTC
1 ATGGTTTCAACTCAATTGCCAAGCAGCCCTCACTCGCCGCTTGTC
*
43685 ATGGTTTCAACTCAATTGCCAAGCAGCCCTCACTCTCCGCTT
1 ATGGTTTCAACTCAATTGCCAAGCAGCCCTCACTCGCCGCTT
43727 TGACTCGCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.20, C:0.36, G:0.16, T:0.29
Consensus pattern (45 bp):
ATGGTTTCAACTCAATTGCCAAGCAGCCCTCACTCGCCGCTTGTC
Found at i:46948 original size:19 final size:20
Alignment explanation
Indices: 46924--46978 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
46914 TGTACAGGCA
46924 GTACAGATGAGATTA-CACT
1 GTACAGATGAGATTAGCACT
* *
46943 GTACAGATTAGATTAGGTACT
1 GTACAGATGAGATTA-GCACT
*
46964 GTACATATGAGATTA
1 GTACAGATGAGATTA
46979 TTAGAGCAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
21 16 0.53
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (20 bp):
GTACAGATGAGATTAGCACT
Found at i:47031 original size:14 final size:14
Alignment explanation
Indices: 47012--47039 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47002 ATTACACTTA
47012 AGGCTCCATTTGAC
1 AGGCTCCATTTGAC
47026 AGGCTCCATTTGAC
1 AGGCTCCATTTGAC
47040 CGATTACACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
AGGCTCCATTTGAC
Found at i:47103 original size:107 final size:107
Alignment explanation
Indices: 46934--47148 Score: 421
Period size: 107 Copynumber: 2.0 Consensus size: 107
46924 GTACAGATGA
*
46934 GATTACACTGTACAGATTAGATTAGGTACTGTACATATGAGATTATTAGAGCAGCGATTGAAACG
1 GATTACACTGTACAGATTAGATTAGGTACTGTACAGATGAGATTATTAGAGCAGCGATTGAAACG
46999 GAGATTACACTTAAGGCTCCATTTGACAGGCTCCATTTGACC
66 GAGATTACACTTAAGGCTCCATTTGACAGGCTCCATTTGACC
47041 GATTACACTGTACAGATTAGATTAGGTACTGTACAGATGAGATTATTAGAGCAGCGATTGAAACG
1 GATTACACTGTACAGATTAGATTAGGTACTGTACAGATGAGATTATTAGAGCAGCGATTGAAACG
47106 GAGATTACACTTAAGGCTCCATTTGACAGGCTCCATTTGACC
66 GAGATTACACTTAAGGCTCCATTTGACAGGCTCCATTTGACC
47148 G
1 G
47149 GTGCACCGGT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (107 bp):
GATTACACTGTACAGATTAGATTAGGTACTGTACAGATGAGATTATTAGAGCAGCGATTGAAACG
GAGATTACACTTAAGGCTCCATTTGACAGGCTCCATTTGACC
Found at i:47138 original size:14 final size:14
Alignment explanation
Indices: 47119--47146 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47109 ATTACACTTA
47119 AGGCTCCATTTGAC
1 AGGCTCCATTTGAC
47133 AGGCTCCATTTGAC
1 AGGCTCCATTTGAC
47147 CGGTGCACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
AGGCTCCATTTGAC
Found at i:49471 original size:52 final size:54
Alignment explanation
Indices: 49409--49541 Score: 191
Period size: 53 Copynumber: 2.5 Consensus size: 54
49399 CCATATCCCA
**
49409 GATCAGACAACAAATTCAAACCAGAAA-TACAAAAAT-CGAAAGTGGGTTTGAT
1 GATCAGACAACAAATTCAAACCAGAAAGTACAAAAATAAAAAAGTGGGTTTGAT
* * *
49461 GATCAGACAACAAATTCAAA-CAAAAAGTGCAAATATAAAAAAGTGGGTTTGAT
1 GATCAGACAACAAATTCAAACCAGAAAGTACAAAAATAAAAAAGTGGGTTTGAT
*
49514 GATCAGACAACAAATTCAAACAAGAAAG
1 GATCAGACAACAAATTCAAACCAGAAAG
49542 CCTTTAAAAC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
51 5 0.07
52 27 0.38
53 34 0.48
54 5 0.07
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.18
Consensus pattern (54 bp):
GATCAGACAACAAATTCAAACCAGAAAGTACAAAAATAAAAAAGTGGGTTTGAT
Found at i:54862 original size:16 final size:17
Alignment explanation
Indices: 54831--54865 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
54821 ACAAAATGCA
54831 TGTTTAGTTCATTTGTT
1 TGTTTAGTTCATTTGTT
*
54848 TGTTTA-TTTATTTGTT
1 TGTTTAGTTCATTTGTT
54864 TG
1 TG
54866 ATAGGTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.11, C:0.03, G:0.17, T:0.69
Consensus pattern (17 bp):
TGTTTAGTTCATTTGTT
Found at i:59678 original size:76 final size:76
Alignment explanation
Indices: 59542--59684 Score: 166
Period size: 76 Copynumber: 1.9 Consensus size: 76
59532 GACGTTGGCT
* **
59542 GCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGTGGGCAGTG
1 GCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAAATGGGCAGTG
59607 TCACGACTTCA
66 TCACGACTTCA
* * ** *
59618 GCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCAAATGGGCT
1 GCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCAAATGGGCA
59680 GTGTC
63 GTGTC
59685 TTAGCTCATC
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
75 4 0.07
76 46 0.82
77 6 0.11
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.26
Consensus pattern (76 bp):
GCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAAATGGGCAGTG
TCACGACTTCA
Found at i:65690 original size:21 final size:21
Alignment explanation
Indices: 65657--65705 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
65647 GAGAATTGTA
**
65657 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
65677 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
65698 GCATTCCT
1 GC-TTCCT
65706 AAAGCTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:75039 original size:30 final size:29
Alignment explanation
Indices: 74966--75043 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
74956 ACTTGTAGTG
**
74966 TTTGGACGTTTTGCTGCCTGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
*
74995 TTTGGACATTTTGCCCCCTGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
*
75024 TTTGGGATGTTTTGCCCCCT
1 TTT-GGACGTTTTGCCCCCT
75044 CCAGCTAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 29 0.67
30 14 0.33
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.41
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCCTGAACTTCAAT
Found at i:75197 original size:29 final size:29
Alignment explanation
Indices: 75151--75226 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
75141 TTAACCTGAG
* *
75151 GGGGCAAAAAGTCCCAAAATTGAAGTTTAT
1 GGGGCAAAAAGT-CCAAAATTGAAGTTCAA
*
75181 GGGGCAAAATGTCCAAAATTGAAGTTCAA
1 GGGGCAAAAAGTCCAAAATTGAAGTTCAA
* *
75210 GGGGTAAAACGTCCAAA
1 GGGGCAAAAAGTCCAAA
75227 CGCTACAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 30 0.73
30 11 0.27
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (29 bp):
GGGGCAAAAAGTCCAAAATTGAAGTTCAA
Found at i:76706 original size:14 final size:15
Alignment explanation
Indices: 76689--76721 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
76679 ATTCTTAAGA
*
76689 ATTAATTT-ATGAAT
1 ATTAATTTAATAAAT
76703 ATTAATTTAATAAAT
1 ATTAATTTAATAAAT
76718 ATTA
1 ATTA
76722 TTTTTAGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTAATTTAATAAAT
Found at i:76891 original size:86 final size:88
Alignment explanation
Indices: 76774--76939 Score: 246
Period size: 86 Copynumber: 1.9 Consensus size: 88
76764 CATGCTTGGA
* * *
76774 TTTTCTTAAAAATTGGGAGATTTGACTTAGTACGTAATTGTTATATGAACTCATGACATGAGTAA
1 TTTTCTTAAAAATTGGAAGATTTGACTTAGTACATAATTGTTATATGAACTCATGACATAAGTAA
*
76839 GACAT-TTTTTTAATCGATAACT
66 AACATATTTTTTAATCGATAACT
* * *
76861 TTTTCTTAAAGATT-GAAGATTTGACTTAGTATATAATTGTTATATGAATTCATGACATAAGTAA
1 TTTTCTTAAAAATTGGAAGATTTGACTTAGTACATAATTGTTATATGAACTCATGACATAAGTAA
76925 AACATCATTTTTTAA
66 AACAT-ATTTTTTAA
76940 CCCTGCAAAC
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
86 49 0.70
87 13 0.19
88 8 0.11
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.42
Consensus pattern (88 bp):
TTTTCTTAAAAATTGGAAGATTTGACTTAGTACATAATTGTTATATGAACTCATGACATAAGTAA
AACATATTTTTTAATCGATAACT
Found at i:83969 original size:13 final size:13
Alignment explanation
Indices: 83951--83975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83941 TATTATAGTA
83951 TAAGTAAAATTAT
1 TAAGTAAAATTAT
83964 TAAGTAAAATTA
1 TAAGTAAAATTA
83976 GGAATTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TAAGTAAAATTAT
Found at i:84503 original size:1 final size:1
Alignment explanation
Indices: 84497--84522 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
84487 GTCCAACCGC
84497 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
84523 GGTATTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:86447 original size:11 final size:10
Alignment explanation
Indices: 86431--86477 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
86421 AAACTTGTGT
86431 TTGAAGACTCA
1 TTGAAGA-TCA
*
86442 TTGAAGATAA
1 TTGAAGATCA
86452 TTTGAAGAT--
1 -TTGAAGATCA
86461 TTGAAGATCA
1 TTGAAGATCA
86471 TTGAAGA
1 TTGAAGA
86478 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:86466 original size:19 final size:18
Alignment explanation
Indices: 86442--86477 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
86432 TGAAGACTCA
86442 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
86461 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
86478 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:91318 original size:34 final size:34
Alignment explanation
Indices: 91242--91321 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
91232 TCAACAGGGG
*
91242 CATAATAAGTATAGTCATGGCCTCTATAATGGCC
1 CATAATAATTATAGTCATGGCCTCTATAATGGCC
91276 CATAATAATTATAGTCATGGCCTCTATAATGGCC
1 CATAATAATTATAGTCATGGCCTCTATAATGGCC
91310 CATAATAATTAT
1 CATAATAATTAT
91322 TTACAATATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (34 bp):
CATAATAATTATAGTCATGGCCTCTATAATGGCC
Found at i:106825 original size:31 final size:31
Alignment explanation
Indices: 106752--106828 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
106742 TTTTTCTATT
* * * *
106752 TTTAGGCTCAAATTGAGCAATTTTTGAAATG
1 TTTAGACTCAAATTGAGCAACTTCTGAAAGG
* *
106783 TTTA-AGTTCAAATTGAGTAACTTCTGAAAGG
1 TTTAGA-CTCAAATTGAGCAACTTCTGAAAGG
106814 TTTAGACTCAAATTG
1 TTTAGACTCAAATTG
106829 GTGATTTGGC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (31 bp):
TTTAGACTCAAATTGAGCAACTTCTGAAAGG
Found at i:106967 original size:31 final size:29
Alignment explanation
Indices: 106932--107000 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
106922 CAAATTTAGG
*
106932 CTCAAATTGGTGCATTTTAATAAGATTTAAA
1 CTCAAATTGGTGCAGTTT-A-AAGATTTAAA
* * * *
106963 CTCAATTTGGTTCAGTTTAAAGGTTTAGA
1 CTCAAATTGGTGCAGTTTAAAGATTTAAA
106992 CTCAAATTG
1 CTCAAATTG
107001 AGCACATTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 16 0.50
30 1 0.03
31 15 0.47
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (29 bp):
CTCAAATTGGTGCAGTTTAAAGATTTAAA
Found at i:107518 original size:25 final size:25
Alignment explanation
Indices: 107484--107531 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
107474 ATCTTCTTAT
107484 GATCATCTTCTTAATATTAGCGTAA
1 GATCATCTTCTTAATATTAGCGTAA
107509 GATCATCTTCTTAATATTAGCGT
1 GATCATCTTCTTAATATTAGCGT
107532 TGTCATGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (25 bp):
GATCATCTTCTTAATATTAGCGTAA
Found at i:107721 original size:33 final size:33
Alignment explanation
Indices: 107679--107746 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
107669 TACATGTCAA
*
107679 CCCTTAACCCCTGCATATGTAGTTTGCTAAACT
1 CCCTTAACCCCTACATATGTAGTTTGCTAAACT
*
107712 CCCTTAACCCCTACATGTGTAGTTTGCTAAACT
1 CCCTTAACCCCTACATATGTAGTTTGCTAAACT
107745 CC
1 CC
107747 ACTGATGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (33 bp):
CCCTTAACCCCTACATATGTAGTTTGCTAAACT
Found at i:119451 original size:36 final size:33
Alignment explanation
Indices: 119390--119468 Score: 113
Period size: 36 Copynumber: 2.3 Consensus size: 33
119380 CTCATAGTTT
*
119390 TTGCAAAAAAATAATAATAAACTGCCTTTGTAA
1 TTGCAAAAAAATAATAATAAACTGCCTTTATAA
*
119423 TTGCAAAATAAATAAATAAATAATCTGCCTTTATAA
1 TTGCAAAA-AAAT-AAT-AATAAACTGCCTTTATAA
119459 TTGCAAAAAA
1 TTGCAAAAAA
119469 TGAGAGAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
33 8 0.20
34 4 0.10
35 5 0.12
36 24 0.59
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (33 bp):
TTGCAAAAAAATAATAATAAACTGCCTTTATAA
Found at i:122713 original size:30 final size:31
Alignment explanation
Indices: 122677--122747 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 31
122667 ATTGAATCGT
122677 TCAAATCCT-TTGGTTTGAACCTAAGCCTTA
1 TCAAATCCTGTTGGTTTGAACCTAAGCCTTA
122707 TCAAAT-CTGTTGGTTTGAACCTAAGCCTTA
1 TCAAATCCTGTTGGTTTGAACCTAAGCCTTA
122737 TCAAAT-CTGTT
1 TCAAATCCTGTT
122748 ACCAGTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 2 0.05
30 38 0.95
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (31 bp):
TCAAATCCTGTTGGTTTGAACCTAAGCCTTA
Found at i:127022 original size:30 final size:31
Alignment explanation
Indices: 126986--127056 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 31
126976 ATTGAATTGT
126986 TCAAATCCT-TTGGTTTGAACCTAAGCCTTA
1 TCAAATCCTGTTGGTTTGAACCTAAGCCTTA
127016 TCAAAT-CTGTTGGTTTGAACCTAAGCCTTA
1 TCAAATCCTGTTGGTTTGAACCTAAGCCTTA
127046 TCAAAT-CTGTT
1 TCAAATCCTGTT
127057 ACTAGTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 2 0.05
30 38 0.95
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (31 bp):
TCAAATCCTGTTGGTTTGAACCTAAGCCTTA
Found at i:146038 original size:2 final size:2
Alignment explanation
Indices: 146031--146069 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
146021 GAGGAGGAAA
146031 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
146070 GTGACAACAA
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:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:146809 original size:1 final size:1
Alignment explanation
Indices: 146803--146832 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
146793 TGGGACCTGC
146803 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
146833 CCCTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:147230 original size:32 final size:32
Alignment explanation
Indices: 147192--147252 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
147182 TGTAAAACTT
*
147192 TTGAATCGACTATTATA-TCCTTATTTTTCTAA
1 TTGAATCGACCATTATACT-CTTATTTTTCTAA
147224 TTGAATCGACCATTATACTCTTATTTTTC
1 TTGAATCGACCATTATACTCTTATTTTTC
147253 AGACATATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (32 bp):
TTGAATCGACCATTATACTCTTATTTTTCTAA
Found at i:148927 original size:15 final size:15
Alignment explanation
Indices: 148904--148935 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
148894 CCTAATTTGT
148904 AAAAATTAAGTACTG
1 AAAAATTAAGTACTG
*
148919 AAAATTTAAGTACTG
1 AAAAATTAAGTACTG
148934 AA
1 AA
148936 TCTTCATGGC
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:0.53, C:0.06, G:0.12, T:0.28
Consensus pattern (15 bp):
AAAAATTAAGTACTG
Found at i:149212 original size:17 final size:17
Alignment explanation
Indices: 149172--149205 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
149162 ACCTTAGACC
149172 TACTTTTTATTTTCAAT
1 TACTTTTTATTTTCAAT
149189 TACTTTTTATTTTCAAT
1 TACTTTTTATTTTCAAT
149206 GCTTTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TACTTTTTATTTTCAAT
Found at i:150087 original size:13 final size:14
Alignment explanation
Indices: 150069--150098 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
150059 ACCCGTCAAG
150069 CTCAAG-TTTATTT
1 CTCAAGTTTTATTT
150082 CTCAAGTTTTATTT
1 CTCAAGTTTTATTT
150096 CTC
1 CTC
150099 GCTGGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (14 bp):
CTCAAGTTTTATTT
Found at i:151833 original size:2 final size:2
Alignment explanation
Indices: 151828--151860 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
151818 ACACACGCAT
151828 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 T
151861 TTGCACCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:166145 original size:45 final size:45
Alignment explanation
Indices: 166081--166208 Score: 240
Period size: 45 Copynumber: 2.9 Consensus size: 45
166071 AGCAACAATT
166081 AATATTAGC-TTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
*
166125 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
166170 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAG
166209 TAGAATTTAG
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
44 9 0.11
45 73 0.89
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.37
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:170358 original size:27 final size:27
Alignment explanation
Indices: 170310--170365 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
170300 GCTTCACAAA
* *
170310 ATTGGTGTATAGATATATTGATATTGG
1 ATTGGTGTATAGAGATACTGATATTGG
* *
170337 ATTGGTGTATAGCGCTACTGATATTGG
1 ATTGGTGTATAGAGATACTGATATTGG
170364 AT
1 AT
170366 AGGCATTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (27 bp):
ATTGGTGTATAGAGATACTGATATTGG
Found at i:171218 original size:31 final size:31
Alignment explanation
Indices: 171183--171247 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
171173 TTAATGGAAA
171183 TATGAATTCAATAAAGATATTTTTAATAACG
1 TATGAATTCAATAAAGATATTTTTAATAACG
171214 TATGAATTCAATAAAGATATTTTTAATAACG
1 TATGAATTCAATAAAGATATTTTTAATAACG
171245 TAT
1 TAT
171248 ATATTGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (31 bp):
TATGAATTCAATAAAGATATTTTTAATAACG
Found at i:171754 original size:21 final size:21
Alignment explanation
Indices: 171716--171759 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
171706 GGAGATGCCA
* *
171716 AAGATGCCATTTGATCCATTG
1 AAGATGCCATTAGATCCAATG
*
171737 AAGATGCCATTAGGTCCAATG
1 AAGATGCCATTAGATCCAATG
171758 AA
1 AA
171760 AAGAGCAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGATGCCATTAGATCCAATG
Found at i:175298 original size:23 final size:24
Alignment explanation
Indices: 175267--175313 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
175257 TGAGAGGATG
*
175267 ACGTTCTGAAAATTTT-TGGTGGA
1 ACGTACTGAAAATTTTCTGGTGGA
*
175290 ACGTACTGAGAATTTTCTGGTGGA
1 ACGTACTGAAAATTTTCTGGTGGA
175314 GGCCGAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.36
Consensus pattern (24 bp):
ACGTACTGAAAATTTTCTGGTGGA
Found at i:177732 original size:50 final size:50
Alignment explanation
Indices: 177670--177997 Score: 559
Period size: 50 Copynumber: 6.6 Consensus size: 50
177660 CGATCAACTT
* *
177670 CTTCGAATTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
177720 CTTCGAACTGTCTTCCGATTTAATCTTAAAAGAACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
177770 CTTCGAACTGTCTTCTAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
177820 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
177870 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
177920 CTTCGAACTGTCTTCCAATTCAATCTT-AAAGGACCGTCTTCCGCTTGTC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
177969 CTTCGAACTATCTTCCAATTTAATCTTAA
1 CTTCGAACTGTCTTCCAATTCAATCTTAA
177998 TATCTGGTAA
Statistics
Matches: 262, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
49 45 0.17
50 217 0.83
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (50 bp):
CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Done.