Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016842.1 Corchorus olitorius cultivar O-4 contig16875, 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: 84949
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3525 original size:2 final size:2
Alignment explanation
Indices: 3518--3561 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
3508 CAGAAGAGTT
* * *
3518 AG AG AG AG A- AG AG AG GG AG GG AG AG AG AG AG GG 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
3559 AG A
1 AG A
3562 TGGGGTTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3544 original size:12 final size:12
Alignment explanation
Indices: 3518--3560 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
3508 CAGAAGAGTT
*
3518 AGAGAGA-GAAG
1 AGAGAGAGGGAG
*
3529 AGAGGGAGGGAG
1 AGAGAGAGGGAG
3541 AGAGAGAGGGAG
1 AGAGAGAGGGAG
3553 AGAGAGAG
1 AGAGAGAG
3561 ATGGGGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 6 0.21
12 22 0.79
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (12 bp):
AGAGAGAGGGAG
Found at i:16481 original size:12 final size:12
Alignment explanation
Indices: 16464--16488 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16454 GGTCTGACCT
16464 TTAGGGAAAAGG
1 TTAGGGAAAAGG
16476 TTAGGGAAAAGG
1 TTAGGGAAAAGG
16488 T
1 T
16489 CATTTAAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (12 bp):
TTAGGGAAAAGG
Found at i:17761 original size:14 final size:15
Alignment explanation
Indices: 17734--17777 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 15
17724 CGACAAATAT
17734 TACTTACAAAAAAAA
1 TACTTACAAAAAAAA
17749 TACTTACAAAAAAATA
1 TACTTACAAAAAAA-A
17765 TTACTTACAAAAA
1 -TACTTACAAAAA
17778 TTACATACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 14 0.52
16 1 0.04
17 12 0.44
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (15 bp):
TACTTACAAAAAAAA
Found at i:17769 original size:17 final size:17
Alignment explanation
Indices: 17728--17777 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
17718 TGAGGACGAC
17728 AAATATTACTTACAAAA
1 AAATATTACTTACAAAA
17745 AAA-A-TACTTACAAAA
1 AAATATTACTTACAAAA
17760 AAATATTACTTACAAAA
1 AAATATTACTTACAAAA
17777 A
1 A
17778 TTACATACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.45
16 2 0.06
17 15 0.48
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATATTACTTACAAAA
Found at i:17778 original size:15 final size:15
Alignment explanation
Indices: 17728--17778 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
17718 TGAGGACGAC
17728 AAATATTACTTACAA
1 AAATATTACTTACAA
* *
17743 AAAAAATACTTACAAAA
1 AAATATTACTTAC--AA
17760 AAATATTACTTACAA
1 AAATATTACTTACAA
17775 AAAT
1 AAAT
17779 TACATACACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 17 0.57
17 13 0.43
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATATTACTTACAA
Found at i:17780 original size:13 final size:13
Alignment explanation
Indices: 17726--17828 Score: 64
Period size: 13 Copynumber: 7.2 Consensus size: 13
17716 CCTGAGGACG
*
17726 ACAAATATTACTT
1 ACAAAAATTACTT
*
17739 ACAAAAAAAATACTT
1 AC--AAAAATTACTT
17754 ACAAAAAAATATTACTT
1 AC---AAAA-ATTACTT
*
17771 ACAAAAATTACAT
1 ACAAAAATTACTT
*
17784 ACACTAATAATTAACAT
1 ACA--AA-AATT-ACTT
17801 A-AAAAATTACTT
1 ACAAAAATTACTT
*
17813 ACAAAAATTACAT
1 ACAAAAATTACTT
17826 ACA
1 ACA
17829 TGTCTTTGTC
Statistics
Matches: 75, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
12 4 0.05
13 28 0.37
14 6 0.08
15 13 0.17
16 11 0.15
17 13 0.17
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (13 bp):
ACAAAAATTACTT
Found at i:27670 original size:56 final size:56
Alignment explanation
Indices: 27601--27714 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
27591 TTTATTTTGT
* *
27601 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAATATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
*
27657 AGAATAATTAAGTAGAAATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
27713 AG
1 AG
27715 GAAACGAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (56 bp):
AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:29863 original size:43 final size:42
Alignment explanation
Indices: 29729--30059 Score: 413
Period size: 43 Copynumber: 7.8 Consensus size: 42
29719 CAATAACCAA
*
29729 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGC-ATTCTATTAC
* * * *
29772 AAAAGTTCTCAAACACATATATAACACAGAGGCA-TCTATATTC
1 -AAAGTCCCCAAACACATATATAACACAGGGGCATTCTAT-TAC
* *
29815 -TAGTCCCCAAACACATATATAACACATGGGCAATTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGC-ATTCTATTAC
* * * *
29857 AAAGTCCTCAAACACTTATATAACACCGAGGCATT-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATTCTATTA-C
29898 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGC-ATTCTATTAC
* *
29941 AAAGTCCTCAAACACATATATAACACAGAGGCATT-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATTCTATTA-C
29982 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCAT-TCTATTAC
* *
30025 AAAGTCCTCAAACACATATATAACACAGAGGCATT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATT
30060 TCTCCTTATG
Statistics
Matches: 249, Mismatches: 26, Indels: 26
0.83 0.09 0.09
Matches are distributed among these distances:
40 4 0.02
41 92 0.37
42 19 0.08
43 101 0.41
44 33 0.13
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATTCTATTAC
Found at i:30087 original size:84 final size:84
Alignment explanation
Indices: 29729--30060 Score: 560
Period size: 84 Copynumber: 3.9 Consensus size: 84
29719 CAATAACCAA
* *
29729 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTTCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATAT
*
29794 AACACAGAGGCATCTATATTC
65 AACACAGAGGCATTTATA-TC
* * *
29815 -TAGTCCCCAAACACATATATAACACATGGGCAATTCTATTACAAAGTCCTCAAACACTTATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
*
29879 ACACCGAGGCATTTATATC
66 ACACAGAGGCATTTATATC
29898 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
29963 ACACAGAGGCATTTATATC
66 ACACAGAGGCATTTATATC
29982 AAAGTCCCCAAACACATATATAACACAGGGGC-ATCTCTATTACAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATAT
30046 AACACAGAGGCATTT
65 AACACAGAGGCATTT
30061 CTCCTTATGG
Statistics
Matches: 233, Mismatches: 11, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
83 4 0.02
84 190 0.82
85 39 0.17
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATTTATATC
Found at i:44263 original size:149 final size:151
Alignment explanation
Indices: 43988--44301 Score: 524
Period size: 149 Copynumber: 2.1 Consensus size: 151
43978 TTTTGTCTGA
*
43988 TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCAATC
1 TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTCTTA--TT-GGCCAATC
*
44053 GGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
63 GAGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
*
44118 GTTTATGGCCTAACTATAATTATT
128 GTTTATGGCCTAACTATAATCATT
*
44142 TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTCTTA-T-GCCTATCGAG
1 TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTCTTATTGGCCAATCGAG
* *
44205 GCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCGATGCTTTTCTTTCCATTGTT
66 GCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
44270 TATGGCCTAACTATAATCATT
131 TATGGCCTAACTATAATCATT
*
44291 TTGATGAGATT
1 TTGGTGAGATT
44302 TTGTGTTTAT
Statistics
Matches: 153, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
149 101 0.66
151 1 0.01
154 51 0.33
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (151 bp):
TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTCTTATTGGCCAATCGAG
GCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
TATGGCCTAACTATAATCATT
Found at i:45491 original size:107 final size:107
Alignment explanation
Indices: 45369--45576 Score: 346
Period size: 107 Copynumber: 1.9 Consensus size: 107
45359 ATTTGAACTT
* * *
45369 TTTTTGTCCTTTTCTGTCTTTTCTCACTTGTCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAA
1 TTTTTGTCATCTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAA
*
45434 CCAGTTCTTGC-CTTTGAGGCCTTTTTTGTAATTATCATTTCC
66 CCAGTTCTTGCTC-TTGAGCCCTTTTTTGTAATTATCATTTCC
* *
45476 TTTTTGTCATCTTCTGTCTTTTCTCATTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAG
1 TTTTTGTCATCTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAA
45541 CCAGTTCTTGCTCTTGAGCCCTTTTTTGTAATTATC
66 CCAGTTCTTGCTCTTGAGCCCTTTTTTGTAATTATC
45577 TGTTTTCTTT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
107 93 0.99
108 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (107 bp):
TTTTTGTCATCTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAA
CCAGTTCTTGCTCTTGAGCCCTTTTTTGTAATTATCATTTCC
Found at i:45674 original size:57 final size:56
Alignment explanation
Indices: 45581--45697 Score: 207
Period size: 57 Copynumber: 2.1 Consensus size: 56
45571 ATTATCTGTT
* *
45581 TTCTTTCTCACAATAAATGTTATAATAAATCCTATCCCCACTATCTCTACTTAATTA
1 TTCTTTCACACAATAAATGTTATAATAAATCATATCCCC-CTATCTCTACTTAATTA
45638 TTCTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTA
1 TTCTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTA
45694 TTCT
1 TTCT
45698 ATAAAATAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 21 0.36
57 37 0.64
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (56 bp):
TTCTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTA
Found at i:45710 original size:57 final size:57
Alignment explanation
Indices: 45592--45710 Score: 177
Period size: 57 Copynumber: 2.1 Consensus size: 57
45582 TCTTTCTCAC
* * * * *
45592 AATAAATGTTATAATAAATCCTATCCCCACTATCTCTACTTAATTATTCTTTCACAC
1 AATAAATGTTATAATAAATCATATCCCCACTATCTCTACTTAATTATTCTATAAAAA
45649 AATAAATGTTATAATAAATCATATCCCC-CTATCTCTACTTAATTATTCTATAAAATA
1 AATAAATGTTATAATAAATCATATCCCCACTATCTCTACTTAATTATTCTATAAAA-A
45706 AATAA
1 AATAA
45711 TATTTTCTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 24 0.43
57 32 0.57
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (57 bp):
AATAAATGTTATAATAAATCATATCCCCACTATCTCTACTTAATTATTCTATAAAAA
Found at i:63742 original size:17 final size:17
Alignment explanation
Indices: 63720--63755 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
63710 TGATTTGTAA
63720 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
63737 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
63754 AG
1 AG
63756 CTCTATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:76549 original size:37 final size:37
Alignment explanation
Indices: 76494--76568 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
76484 GTCAACCTAA
* * *
76494 ATGACTATGTCAACCTAATTAAAACGTGCATGTGACT
1 ATGACTATGCCAAACTAATTAAAACGTGCACGTGACT
76531 ATGACTATGCCAAACTAATTAAAACGTGCACGTGACT
1 ATGACTATGCCAAACTAATTAAAACGTGCACGTGACT
76568 A
1 A
76569 AAACATACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (37 bp):
ATGACTATGCCAAACTAATTAAAACGTGCACGTGACT
Found at i:77119 original size:42 final size:42
Alignment explanation
Indices: 77072--77188 Score: 207
Period size: 42 Copynumber: 2.8 Consensus size: 42
77062 GAGTTCCAAT
77072 CTTGAAGATGCTACACCGAGTCATCTGATTCACCAAATCCCA
1 CTTGAAGATGCTACACCGAGTCATCTGATTCACCAAATCCCA
* *
77114 CTTGAAGATGCTACACCGAGTCATCTGATTCACCGAGTCCCA
1 CTTGAAGATGCTACACCGAGTCATCTGATTCACCAAATCCCA
77156 CTTGAAGATGCTACACCGAGTCATCTGAATTCA
1 CTTGAAGATGCTACACCGAGTCATCTG-ATTCA
77189 TCTTTGAAGA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
42 67 0.93
43 5 0.07
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (42 bp):
CTTGAAGATGCTACACCGAGTCATCTGATTCACCAAATCCCA
Found at i:77203 original size:35 final size:35
Alignment explanation
Indices: 77157--77444 Score: 436
Period size: 35 Copynumber: 8.2 Consensus size: 35
77147 CGAGTCCCAC
* *
77157 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
1 TTGAAGATGCTACACTGAGTCATCTG-ATTCTAACT
* * * *
77192 TTGAAGATGCTACACCGAGTCATCCGAGTTC-ATCC
1 TTGAAGATGCTACACTGAGTCATCTGA-TTCTAACT
77227 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
* *
77262 TTGAACACGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
77297 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
* *
77332 TTGAAGACGCTACACCGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
*
77367 TTGAAGACGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
*
77402 TTGAAGACGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
77437 TTGAAGAT
1 TTGAAGAT
77445 AAACCTAAAT
Statistics
Matches: 237, Mismatches: 14, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
34 4 0.02
35 233 0.98
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (35 bp):
TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
Found at i:77541 original size:50 final size:50
Alignment explanation
Indices: 77481--77995 Score: 841
Period size: 50 Copynumber: 10.3 Consensus size: 50
77471 GACTGGCCAT
* * * *
77481 ACTGGATCACTGGAAGATAAACTTAAACCACTGTAAACTTGATTTATCGC
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
77531 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
* * *
77581 ACTGGATCACTTGAAGAAAAACTTGAACCACTGTAAACTTGATTTATCGC
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
* * *
77631 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAACTTGATTTATCGT
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
* *
77681 ACTGGATCACTTGAAGAAAATCTTAAACCACTGTAAATTTGATTGATCAC
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
* * * *
77731 ACTAGATCACTTGAAGAAAAAATTAAACCACTGTAAACTTGATTTATCGC
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
77781 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
*
77831 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCAC
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
* *
77881 ACTGGAGCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCAC
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
*
77931 ACTGGATCACTTGAAGAAAAACTTAGACCACTGTAAATTTGATTGATCGC
1 ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
*
77981 ACTGAATCACTTGAA
1 ACTGGATCACTTGAA
77996 ACTAACTGAG
Statistics
Matches: 435, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 435 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (50 bp):
ACTGGATCACTTGAAGAAAAACTTAAACCACTGTAAATTTGATTGATCGC
Found at i:78025 original size:35 final size:35
Alignment explanation
Indices: 77975--78391 Score: 247
Period size: 35 Copynumber: 12.4 Consensus size: 35
77965 AAATTTGATT
* * *
77975 GATCGCACTGAATCACTTGAAACTAACTGAGGAAA
1 GATCGCCCTGGATCACTTGAAACTAACTGAAGAAA
* * *
78010 GATCGCCCCGGATCACTTGAAACTGACTGAACAAA
1 GATCGCCCTGGATCACTTGAAACTAACTGAAGAAA
* **
78045 GATCGGCCC-GGATCAATTGACCCTAACTGAAGAAA
1 GATC-GCCCTGGATCACTTGAAACTAACTGAAGAAA
* * *
78080 GATCGCCTTGGATCAAC-TG-GAGTAAACTGAAGAAA
1 GATCGCCCTGGATC-ACTTGAAACT-AACTGAAGAAA
* * *
78115 GACCGCCCTGGGT--C----AACTGA-T--AGAAA
1 GATCGCCCTGGATCACTTGAAACTAACTGAAGAAA
* *
78141 GATCGCCCTGGATCAGTTGAAACTAATTGAAGAAA
1 GATCGCCCTGGATCACTTGAAACTAACTGAAGAAA
* * *
78176 GATCGCCCTGAATCAGTTGAAACTAATTGAAGAAA
1 GATCGCCCTGGATCACTTGAAACTAACTGAAGAAA
* * *
78211 GATCGCCCTGGATCAATT-AAAGTAAACTGAAGAAT
1 GATCGCCCTGGATCACTTGAAACT-AACTGAAGAAA
* * *
78246 GATCGCCCTGGATCAAC-T-AAAGTAAACTGACGAGA
1 GATCGCCCTGGATC-ACTTGAAACT-AACTGAAGAAA
* * *
78281 GACCACCCTAGG-T--C----AACTGA---AAGAAA
1 GATCGCCCT-GGATCACTTGAAACTAACTGAAGAAA
* * *
78307 GATCGCCCTGGAGCAGTTGAAACTAATTGAAGAAA
1 GATCGCCCTGGATCACTTGAAACTAACTGAAGAAA
* * * *
78342 GATCGCTCTGGATCACTTG-AAGTAAACTAAAGAAT
1 GATCGCCCTGGATCACTTGAAACT-AACTGAAGAAA
*
78377 GATCGCCCTAGATCA
1 GATCGCCCTGGATCA
78392 ACTGAAGTAA
Statistics
Matches: 299, Mismatches: 56, Indels: 54
0.73 0.14 0.13
Matches are distributed among these distances:
25 2 0.01
26 27 0.09
28 1 0.00
29 2 0.01
30 5 0.02
32 12 0.04
33 1 0.00
34 11 0.04
35 230 0.77
36 8 0.03
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (35 bp):
GATCGCCCTGGATCACTTGAAACTAACTGAAGAAA
Found at i:78162 original size:131 final size:131
Alignment explanation
Indices: 78006--78263 Score: 347
Period size: 131 Copynumber: 2.0 Consensus size: 131
77996 ACTAACTGAG
* * **
78006 GAAAGATCGCCCCGGATCACTTGAAACTGACTGAACAAAGATCGGCCC-GGATCAATTGACCCTA
1 GAAAGATCGCCCCGGATCACTTGAAACTAACTGAACAAAGATC-GCCCTGAATCAATTGAAACTA
* ** *
78070 ACTGAAGAAAGATCGCCTTGGATCAACTGGAGTAAACTGAAGAAAGACCGCCCTGGGTCAACTGA
65 ACTGAAGAAAGATCGCCCTGGATCAACTAAAGTAAACTGAAGAAAGACCGCCCTGGATCAACTGA
78135 TA
130 TA
* * * * *
78137 GAAAGATCGCCCTGGATCAGTTGAAACTAATTGAAGAAAGATCGCCCTGAATCAGTTGAAACTAA
1 GAAAGATCGCCCCGGATCACTTGAAACTAACTGAACAAAGATCGCCCTGAATCAATTGAAACTAA
* * * *
78202 TTGAAGAAAGATCGCCCTGGATCAATTAAAGTAAACTGAAGAATGATCGCCCTGGATCAACT
66 CTGAAGAAAGATCGCCCTGGATCAACTAAAGTAAACTGAAGAAAGACCGCCCTGGATCAACT
78264 AAAGTAAACT
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
130 4 0.04
131 105 0.96
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (131 bp):
GAAAGATCGCCCCGGATCACTTGAAACTAACTGAACAAAGATCGCCCTGAATCAATTGAAACTAA
CTGAAGAAAGATCGCCCTGGATCAACTAAAGTAAACTGAAGAAAGACCGCCCTGGATCAACTGAT
A
Found at i:78272 original size:166 final size:166
Alignment explanation
Indices: 77975--78464 Score: 567
Period size: 166 Copynumber: 3.0 Consensus size: 166
77965 AAATTTGATT
* * * * * * *
77975 GATCGCACTGAATCACTTGAAACTAACTGAGGAAAGATCGCCCCGGATCACTTGAAACTGACTGA
1 GATCGCCCTGGATCAGTTGAAACTAATTGAAGAAAGATCGCCCTGGATCACTTGAAACTAACTGA
* *** *
78040 ACAAAGATCGGCCC-GGATCAATTGACCCT-AACTGAAGAAAGATCGCCTTGGATCAACTGGAGT
66 AGAAAGATC-GCCCTGGATCAATT-AAAGTAAACTGAAGAAAGATCGCCTTGGATCAACTGAAGT
*
78103 AAACTGAAGAAAGACCGCCCTGGGTCAACTGATAGAAA
129 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAAGAAA
* * *
78141 GATCGCCCTGGATCAGTTGAAACTAATTGAAGAAAGATCGCCCTGAATCAGTTGAAACTAATTGA
1 GATCGCCCTGGATCAGTTGAAACTAATTGAAGAAAGATCGCCCTGGATCACTTGAAACTAACTGA
* * *
78206 AGAAAGATCGCCCTGGATCAATTAAAGTAAACTGAAGAATGATCGCCCTGGATCAACTAAAGTAA
66 AGAAAGATCGCCCTGGATCAATTAAAGTAAACTGAAGAAAGATCGCCTTGGATCAACTGAAGTAA
* * * *
78271 ACTGACGAGAGACCACCCTAGGTCAACTGAAAGAAA
131 ACTGAAGAAAGACCGCCCTGGGTCAACTGAAAGAAA
* * * *
78307 GATCGCCCTGGAGCAGTTGAAACTAATTGAAGAAAGATCGCTCTGGATCACTTG-AAGTAAACTA
1 GATCGCCCTGGATCAGTTGAAACTAATTGAAGAAAGATCGCCCTGGATCACTTGAAACT-AACTG
* * * * * * * *
78371 AAGAATGATCGCCCTAGATCAACTGAAGTAAACTAAATAAAAACCGCCTTAGG-TCAACTGAAGT
65 AAGAAAGATCGCCCTGGATCAATTAAAGTAAACTGAAGAAAGATCGCCTT-GGATCAACTGAAGT
* *
78435 AAA-TCGAAGAAGGACCGCCCTGGGTTAACT
129 AAACT-GAAGAAAGACCGCCCTGGGTCAACT
78465 TGAGAATAGT
Statistics
Matches: 272, Mismatches: 47, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
165 10 0.04
166 260 0.96
167 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (166 bp):
GATCGCCCTGGATCAGTTGAAACTAATTGAAGAAAGATCGCCCTGGATCACTTGAAACTAACTGA
AGAAAGATCGCCCTGGATCAATTAAAGTAAACTGAAGAAAGATCGCCTTGGATCAACTGAAGTAA
ACTGAAGAAAGACCGCCCTGGGTCAACTGAAAGAAA
Found at i:78386 original size:96 final size:96
Alignment explanation
Indices: 78205--78397 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
78195 AAACTAATTG
* * *
78205 AAGAAAGATCGCCCTGGATCAATTAAAGTAAACTGAAGAATGATCGCCCTGGATCAACTAAAGTA
1 AAGAAAGATCGCCCTGGAGCAATTAAACTAAACTGAAGAAAGATCGCCCTGGATCAACTAAAGTA
* * *
78270 AACTGACGAGAGACCACCCTAGGTCAACTGA
66 AACTAAAGAGAGACCACCCTAGATCAACTGA
* * * *
78301 AAGAAAGATCGCCCTGGAGCAGTTGAAACT-AATTGAAGAAAGATCGCTCTGGATC-ACTTGAAG
1 AAGAAAGATCGCCCTGGAGCAATT-AAACTAAACTGAAGAAAGATCGCCCTGGATCAAC-TAAAG
* *
78364 TAAACTAAAGA-ATGATCGCCCTAGATCAACTGA
64 TAAACTAAAGAGA-GACCACCCTAGATCAACTGA
78397 A
1 A
78398 GTAAACTAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 3 0.04
96 75 0.91
97 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (96 bp):
AAGAAAGATCGCCCTGGAGCAATTAAACTAAACTGAAGAAAGATCGCCCTGGATCAACTAAAGTA
AACTAAAGAGAGACCACCCTAGATCAACTGA
Found at i:78398 original size:35 final size:35
Alignment explanation
Indices: 78336--78437 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 35
78326 AAACTAATTG
* *
78336 AAGAAAGATCGCTCTGGATC-ACTTGAAGTAAACTA
1 AAGAAAGATCGCCCTAGATCAAC-TGAAGTAAACTA
*
78371 AAGAATGATCGCCCTAGATCAACTGAAGTAAACTA
1 AAGAAAGATCGCCCTAGATCAACTGAAGTAAACTA
* * * * *
78406 AATAAAAACCGCCTTAGGTCAACTGAAGTAAA
1 AAGAAAGATCGCCCTAGATCAACTGAAGTAAA
78438 TCGAAGAAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 55 0.96
36 2 0.04
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.21
Consensus pattern (35 bp):
AAGAAAGATCGCCCTAGATCAACTGAAGTAAACTA
Found at i:78424 original size:131 final size:131
Alignment explanation
Indices: 78170--78432 Score: 391
Period size: 131 Copynumber: 2.0 Consensus size: 131
78160 AAACTAATTG
*
78170 AAGAAAGATCGCCCTGAATCAGTTGAAACTAATTGAAGAAAGATCGCCCTGGATCAATTAAAGTA
1 AAGAAAGATCGCCCTGAAGCAGTTGAAACTAATTGAAGAAAGATCGCCCTGGATCAATTAAAGTA
* * * * * *
78235 AACTGAAGAATGATCGCCCTGGATCAACTAAAGTAAACTGACGAGAGACCACCCTAGGTCAACTG
66 AACTAAAGAATGATCGCCCTAGATCAACTAAAGTAAACTAAAGAAAAACCACCCTAGGTCAACTG
78300 A
131 A
* * * *
78301 AAGAAAGATCGCCCTGGAGCAGTTGAAACTAATTGAAGAAAGATCGCTCTGGATCACTTGAAGTA
1 AAGAAAGATCGCCCTGAAGCAGTTGAAACTAATTGAAGAAAGATCGCCCTGGATCAATTAAAGTA
* * * *
78366 AACTAAAGAATGATCGCCCTAGATCAACTGAAGTAAACTAAATAAAAACCGCCTTAGGTCAACTG
66 AACTAAAGAATGATCGCCCTAGATCAACTAAAGTAAACTAAAGAAAAACCACCCTAGGTCAACTG
78431 A
131 A
78432 A
1 A
78433 GTAAATCGAA
Statistics
Matches: 117, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
131 117 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (131 bp):
AAGAAAGATCGCCCTGAAGCAGTTGAAACTAATTGAAGAAAGATCGCCCTGGATCAATTAAAGTA
AACTAAAGAATGATCGCCCTAGATCAACTAAAGTAAACTAAAGAAAAACCACCCTAGGTCAACTG
A
Found at i:79546 original size:12 final size:12
Alignment explanation
Indices: 79504--79546 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
79494 TTCTTATTTC
79504 TCTTTTTTCA-T
1 TCTTTTTTCATT
**
79515 AATTTTTTCATT
1 TCTTTTTTCATT
*
79527 TCATTTTTCATT
1 TCTTTTTTCATT
79539 TCTTTTTT
1 TCTTTTTT
79547 GATTAGTTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (12 bp):
TCTTTTTTCATT
Found at i:82301 original size:9 final size:9
Alignment explanation
Indices: 82287--82312 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
82277 TGTAAACATC
82287 AAAACAAAT
1 AAAACAAAT
82296 AAAACAAAT
1 AAAACAAAT
82305 AAAACAAA
1 AAAACAAA
82313 GCAACCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.12, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAACAAAT
Done.