Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2069
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: 14451
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Found at i:247 original size:33 final size:33
Alignment explanation
Indices: 210--276 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
200 ATTTCCGATT
210 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
243 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
276 T
1 T
277 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:248 original size:13 final size:13
Alignment explanation
Indices: 230--254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220 CATAAAATGT
230 TGTATCGATACAA
1 TGTATCGATACAA
243 TGTATCGATACA
1 TGTATCGATACA
255 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:390 original size:51 final size:52
Alignment explanation
Indices: 331--445 Score: 146
Period size: 51 Copynumber: 2.2 Consensus size: 52
321 TCGATACAAT
*** *
331 TGTATCGATACACTGAT-CTTTGTATCGATGCATGCAGGC-AATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCGATACATGC-GGCAAATTTGCCCAGA
**
382 TGTATCGATACA-TTTTAAAATGTATCGATACATGCGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCGGCAAATTTGCCCAGA
433 TGTATCGATACAC
1 TGTATCGATACAC
446 ACTATTAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
50 5 0.09
51 50 0.91
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTGATAAAATGTATCGATACATGCGGCAAATTTGCCCAGA
Found at i:3165 original size:16 final size:17
Alignment explanation
Indices: 3144--3176 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3134 AAAGGGGATC
3144 ATAAATCAAAAT-AATG
1 ATAAATCAAAATCAATG
*
3160 ATAAATCGAAATCAATG
1 ATAAATCAAAATCAATG
3177 CAAACCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.24
Consensus pattern (17 bp):
ATAAATCAAAATCAATG
Found at i:8717 original size:31 final size:31
Alignment explanation
Indices: 8681--8765 Score: 111
Period size: 30 Copynumber: 2.8 Consensus size: 31
8671 CAAATACCTT
8681 TTCAAAGTCCACGACTCAGTGGCATTTTTGTC
1 TTCAAAGTCCACGACTCAGTGGCATTTTT-TC
8713 -TCAAAGTCCACGACT-AGTGGCATTTTTTC
1 TTCAAAGTCCACGACTCAGTGGCATTTTTTC
* * * *
8742 TTTAAAGCCCACAACTCTGTGGCA
1 TTCAAAGTCCACGACTCAGTGGCA
8766 CACTTTTTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.04
30 24 0.51
31 21 0.45
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (31 bp):
TTCAAAGTCCACGACTCAGTGGCATTTTTTC
Found at i:8798 original size:34 final size:35
Alignment explanation
Indices: 8742--9441 Score: 601
Period size: 34 Copynumber: 20.7 Consensus size: 35
8732 GCATTTTTTC
*
8742 TTTAAAGCCCACAACTCTGTGGCACACTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTTCTT
* * * *
8777 TTTAAAACCCACAA-TTCGTGGCAC-TTTTTTCATC
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTTC-TT
* *
8811 TTT-AAGTCCACAACTCCGTGGCAC-C-----C-G
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTTCTT
*
8838 TTT-AAGCCCACAACTCCGTGGCAAACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACA-CTTTTTCTT
8873 TTTAAAGCCCACAACTCCGTGGCA-ACCTTTTTC-T
1 TTTAAAGCCCACAACTCCGTGGCACA-CTTTTTCTT
* *
8907 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTT
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTT--CTT
* *
8944 TTCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTG
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTTCTT
*
8978 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCT
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTTCT-T
*
9014 TTTCAAAGCCCACGACTCCGTGG--CAC----TC--
1 TTT-AAAGCCCACAACTCCGTGGCACACTTTTTCTT
*
9042 TTTAAAGCCCACAACTCCGTGGCA-ACCTTCTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACA-CTTTTTCTT
* * *
9077 TTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTT
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTT--CTT
* *
9114 TTCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTG
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTTCTT
*
9148 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCT
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTTCT-T
*
9184 TTTCAAAGCCCACGACTCCGTGG--CAC----TC--
1 TTT-AAAGCCCACAACTCCGTGGCACACTTTTTCTT
*
9212 TTTAAAGCCCACAACTCTGTGG--CACTTTCTTCTTT
1 TTTAAAGCCCACAACTCCGTGGCACACTTT-TTC-TT
* *
9247 TCAATTCAAAGCCCACGACTCTGTGG--CAC----TCTT
1 T---TT-AAAGCCCACAACTCCGTGGCACACTTTTTCTT
*
9280 TTTAAAGCCCACAACTCCGTGGCAC-C-TTTTCTG
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTTCTT
*
9313 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTT--CTT
*
9350 TTCAAAGCCCACAACTCCGTGG--CACTTTTTC-T
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTTCTT
* *
9382 TTTAAAGCCCACAAATCCGTGGCACTCTTTTTCCCTT
1 TTTAAAGCCCACAACTCCGTGGCACACTTTTT--CTT
*
9419 TTT-AAGTCCACAACTCCGTGGCA
1 TTTAAAGCCCACAACTCCGTGGCA
9442 TCTTTCTCCC
Statistics
Matches: 559, Mismatches: 47, Indels: 117
0.77 0.07 0.16
Matches are distributed among these distances:
27 60 0.11
28 7 0.01
29 20 0.04
30 3 0.01
31 5 0.01
32 23 0.04
33 48 0.09
34 114 0.20
35 84 0.15
36 58 0.10
37 114 0.20
38 2 0.00
39 21 0.04
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.32
Consensus pattern (35 bp):
TTTAAAGCCCACAACTCCGTGGCACACTTTTTCTT
Found at i:8954 original size:37 final size:33
Alignment explanation
Indices: 8736--9446 Score: 668
Period size: 37 Copynumber: 21.1 Consensus size: 33
8726 CTAGTGGCAT
*
8736 TTTTTC-TTTAAAGCCCACAACTCTGTGGCACAC
1 TTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-C
* * *
8769 TTTTTCTTTTTAAAACCCACAA-TTCGTGGCACT
1 TTTTTC-TTTTAAAGCCCACAACTCCGTGGCACC
*
8802 TTTTTCATCTTT-AAGTCCACAACTCCGTGGCACC
1 TTTTTC-T-TTTAAAGCCCACAACTCCGTGGCACC
*
8836 -----CGTTT-AAGCCCACAACTCCGTGGCAAACC
1 TTTTTCTTTTAAAGCCCACAACTCCGTGGC--ACC
8865 TTTTTCTTTTTAAAGCCCACAACTCCGTGGCAACC
1 TTTTTC-TTTTAAAGCCCACAACTCCGTGGC-ACC
*
8900 TTTTTCTTTTAAAGCCCACAACTCTGTGGCACTC
1 TTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-C
8934 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACC
1 TTTTT--CTTTT-AAAGCCCACAACTCCGTGGCACC
8970 TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTC
1 TTTTTCT-TTTAAAGCCCACAACTCCGTGGCAC-C
*
9005 TTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-C
1 -TTTT-TCTTTT-AAAGCCCACAACTCCGTGGCACC
9040 ----TC-TTTAAAGCCCACAACTCCGTGGCAACC
1 TTTTTCTTTTAAAGCCCACAACTCCGTGGC-ACC
* *
9069 TTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTC
1 TTTTTCTTTT-AAAGCCCACAACTCCGTGGCAC-C
9104 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACC
1 TTTTT--CTTTT-AAAGCCCACAACTCCGTGGCACC
9140 TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTC
1 TTTTTCT-TTTAAAGCCCACAACTCCGTGGCAC-C
*
9175 TTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-C
1 -TTTT-TCTTTT-AAAGCCCACAACTCCGTGGCACC
*
9210 ----TC-TTTAAAGCCCACAACTCTGTGGCA-C
1 TTTTTCTTTTAAAGCCCACAACTCCGTGGCACC
* *
9237 TTTCTTCTTTTCAATTCAAAGCCCACGACTCTGTGGCA-C
1 TTT-TTC--TT---TT-AAAGCCCACAACTCCGTGGCACC
*
9276 --TCT-TTTTAAAGCCCACAACTCCGTGGCACC
1 TTTTTCTTTTAAAGCCCACAACTCCGTGGCACC
9306 -TTTTCTGTTTAAAGCCCACAACTCCGTGGCACTC
1 TTTTTCT-TTTAAAGCCCACAACTCCGTGGCAC-C
9340 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCA-C
1 TTTTT--CTTTT-AAAGCCCACAACTCCGTGGCACC
*
9375 TTTTTCTTTTAAAGCCCACAAATCCGTGGCACTC
1 TTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-C
* * *
9409 TTTTTCCCTTTTTAAGTCCACAACTCCGTGGCATC
1 TTTTT--CTTTTAAAGCCCACAACTCCGTGGCACC
9444 TTT
1 TTT
9447 CTCCCTTCTC
Statistics
Matches: 583, Mismatches: 32, Indels: 124
0.79 0.04 0.17
Matches are distributed among these distances:
27 60 0.10
28 7 0.01
29 28 0.05
30 3 0.01
31 2 0.00
32 23 0.04
33 57 0.10
34 110 0.19
35 75 0.13
36 77 0.13
37 118 0.20
38 2 0.00
39 21 0.04
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
TTTTTCTTTTAAAGCCCACAACTCCGTGGCACC
Found at i:8960 original size:71 final size:67
Alignment explanation
Indices: 8729--9446 Score: 680
Period size: 71 Copynumber: 10.7 Consensus size: 67
8719 TCCACGACTA
* *
8729 GTGGCA-T-TTTTTC-TTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTTAAAACCCACAA
1 GTGGCACTCTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTC-TTTTAAAGCCCACAA
*
8791 -TTC
64 CTCC
* *
8794 GTGGCACT-TTTTTCATCTTT-AAGTCCACAACTCCGTGGCACC-----CGTTT-AAGCCCACAA
1 GTGGCACTCTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAA
8851 CTCC
64 CTCC
8855 GTGGCAAAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCAACCTTTTTCTTTTAAAGCCCAC
1 GTGGC--ACTCTTTTTC-TTTTAAAGCCCACAACTCCGTGGC-ACCTTTTTCTTTTAAAGCCCAC
*
8919 AACTCT
62 AACTCC
8925 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCAC
1 GTGGCACTCTTTTT--CTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCAC
8990 AACTCC
62 AACTCC
*
8996 GTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-C----TC-TTTAAAGCCCACA
1 GTGGCACTC-TTTT-TCTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACA
9055 ACTCC
63 ACTCC
* *
9060 GTGGCAAC-CTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCC
1 GTGGC-ACTCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT-AAAGCCC
9124 ACAACTCC
60 ACAACTCC
9132 GTGGCAC-CTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCA
1 GTGGCACTCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCAC-C-TTTT-TCTTTT-AAAGCCCA
*
9196 CGACTCC
61 CAACTCC
*
9203 GTGGCA--C----TC-TTTAAAGCCCACAACTCTGTGGCA-CTTTCTTCTTTTCAATTCAAAGCC
1 GTGGCACTCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTT-TTC--TT---TT-AAAGCC
* *
9260 CACGACTCT
59 CACAACTCC
9269 GTGGCACTC----T-TTTTAAAGCCCACAACTCCGTGGCACC-TTTTCTGTTTAAAGCCCACAAC
1 GTGGCACTCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAAC
9328 TCC
65 TCC
9331 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCA-CTTTTTCTTTTAAAGCCCACA
1 GTGGCACTCTTTTT--CTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACA
*
9395 AATCC
63 ACTCC
* * *
9400 GTGGCACTCTTTTTCCCTTTTTAAGTCCACAACTCCGTGGCATCTTT
1 GTGGCACTCTTTTT--CTTTTAAAGCCCACAACTCCGTGGCACCTTT
9447 CTCCCTTCTC
Statistics
Matches: 570, Mismatches: 25, Indels: 112
0.81 0.04 0.16
Matches are distributed among these distances:
60 9 0.02
61 15 0.03
62 54 0.09
63 34 0.06
64 51 0.09
65 9 0.02
66 36 0.06
67 4 0.01
68 68 0.12
69 61 0.11
70 62 0.11
71 134 0.24
72 31 0.05
73 2 0.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (67 bp):
GTGGCACTCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACT
CC
Found at i:9115 original size:170 final size:168
Alignment explanation
Indices: 8873--9467 Score: 841
Period size: 170 Copynumber: 3.5 Consensus size: 168
8863 CCTTTTTCTT
*
8873 TTTAAAGCCCACAACTCCGTGGCAACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
1 TTTAAAGCCCACAACTCCGTGGC-ACCTTCTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
8938 TCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCAC
65 TCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCAC
9003 TCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTC
130 TCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTC
9042 TTTAAAGCCCACAACTCCGTGGCAACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTT
1 TTTAAAGCCCACAACTCCGTGGC-ACCTTCTTCTTTT-AAAGCCCACAACTCTGTGGCACTCTTT
9107 TTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCA
64 TTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCA
9172 CTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTC
129 CTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTC
* * *
9212 TTTAAAGCCCACAACTCTGTGGCACTTTCTTCTTTTCAATTCAAAGCCCACGACTCTGTGGCACT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTTC--TT---TT-AAAGCCCACAACTCTGTGGCACT
9277 C----T---TTTT-AAAGCCCACAACTCCGTGGCACC-TTTTCTGTTTAAAGCCCACAACTCCGT
60 CTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGT
* *
9333 GGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTC
125 GGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCAC----TC
* * * * *
9381 TTTTAAAGCCCACAAATCCGTGGCACTCTTTTTCCCTTTTTAAGTCCACAACTCCGTGGCA-TCT
1 -TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--CTTTTAAAGCCCACAACTCTGTGGCACTCT
* *
9445 TTCTCCCTTCTCTAAAGCCCACA
62 TTTTCCCTTTTC-AAAGCCCACA
9468 CAAGTCGGTG
Statistics
Matches: 388, Mismatches: 15, Indels: 40
0.88 0.03 0.09
Matches are distributed among these distances:
165 67 0.17
166 25 0.06
167 21 0.05
168 2 0.01
169 46 0.12
170 179 0.46
171 8 0.02
173 4 0.01
174 26 0.07
175 10 0.03
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (168 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACT
CTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTC
Found at i:9488 original size:33 final size:33
Alignment explanation
Indices: 9450--9621 Score: 294
Period size: 33 Copynumber: 5.2 Consensus size: 33
9440 CATCTTTCTC
9450 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
9483 CCTTCTCTAAAGCCCACAC-AGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
9515 CCCTTCTCTAAAGCCCACACAAGTCGGTGGC-AA
1 -CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
9548 CCTTCCTCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTT-CTCTAAAGCCCACACAAGTCGGTGGCAAA
*
9582 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CC-TTCTCTAAAGCCCACACAAGTCGGTGGCAAA
9616 CCTTCT
1 CCTTCT
9622 AAGCCCAATA
Statistics
Matches: 133, Mismatches: 1, Indels: 10
0.92 0.01 0.07
Matches are distributed among these distances:
32 17 0.13
33 70 0.53
34 44 0.33
35 2 0.02
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.19
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
Found at i:9557 original size:66 final size:66
Alignment explanation
Indices: 9449--9628 Score: 303
Period size: 67 Copynumber: 2.7 Consensus size: 66
9439 GCATCTTTCT
9449 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACAC-AGTCGGTGGCA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGC-AACCTTCTCTAAAGCCCACACAAGTCGGTGGCA
9513 AA
65 AA
9515 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTCCTCTAAAGCCCACACAAGTCGGTGGCA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTT-CTCTAAAGCCCACACAAGTCGGTGGCA
9580 AA
65 AA
* *
9582 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCT-TCT-AAGCCCA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTCTCTAAAGCCCA
9629 ATATAGCTAG
Statistics
Matches: 110, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
64 7 0.06
65 9 0.08
66 46 0.42
67 48 0.44
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.18
Consensus pattern (66 bp):
CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
A
Found at i:9685 original size:49 final size:49
Alignment explanation
Indices: 9621--10191 Score: 793
Period size: 49 Copynumber: 11.7 Consensus size: 49
9611 GCAACCCTTC
* * * * *
9621 TAAGCCCAATATAGCTAGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
9670 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
9719 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
9768 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
9817 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
9866 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
9915 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCAACTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
9963 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
10012 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCA-CCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
10059 TAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
10102 TAAGTCCAATATAGCTGGCCTTGAATCA-CAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCA-CAT-T-GGCACC--TT-CATCTT
*
10156 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
10192 ACATCCTTTT
Statistics
Matches: 464, Mismatches: 44, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
42 2 0.00
43 31 0.07
44 2 0.00
45 4 0.01
47 40 0.09
48 49 0.11
49 299 0.64
52 2 0.00
53 1 0.00
54 32 0.07
55 2 0.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:10119 original size:43 final size:43
Alignment explanation
Indices: 10009--10147 Score: 190
Period size: 47 Copynumber: 3.1 Consensus size: 43
9999 GCACCTTCAT
10009 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
*
10052 CTCACCTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCAC
1 CT----TTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
*
10099 CTTTAAGTCCAATATAGCTGGCCTTGAATCA-CAGCATATCGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA-CAT-T-GGCAC
10144 CTTT
1 CTTT
10148 TCCATCTTTA
Statistics
Matches: 86, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
42 2 0.02
43 32 0.37
44 1 0.01
45 9 0.10
47 42 0.49
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:10203 original size:54 final size:55
Alignment explanation
Indices: 10099--10239 Score: 155
Period size: 54 Copynumber: 2.6 Consensus size: 55
10089 ACATTGGCAC
*
10099 CTTTAAGTCCAATATAGCTGGCCTTGAATCACAGCATATCGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCACAGCATATCGACACCTTTTCACAT
* *
10153 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCA-CAT-T-GACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA-CAGCATATCGACA-CC-TTTTCA-CAT
* * * *
10209 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
10240 ACATATTGGC
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
52 3 0.04
53 3 0.04
54 37 0.51
55 2 0.03
56 28 0.38
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCACAGCATATCGACACCTTTTCACAT
Found at i:11074 original size:33 final size:33
Alignment explanation
Indices: 11037--11103 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11027 TTTCAACATT
11037 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
11070 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
11103 T
1 T
11104 TTAAGCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:11075 original size:13 final size:13
Alignment explanation
Indices: 11057--11081 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11047 CATAAAATGT
11057 TGTATCGATACAA
1 TGTATCGATACAA
11070 TGTATCGATACA
1 TGTATCGATACA
11082 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11162 original size:13 final size:13
Alignment explanation
Indices: 11144--11168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11134 ATTACTCAAA
11144 TGTATCGATACAT
1 TGTATCGATACAT
11157 TGTATCGATACA
1 TGTATCGATACA
11169 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11203 original size:87 final size:83
Alignment explanation
Indices: 11057--11240 Score: 201
Period size: 87 Copynumber: 2.2 Consensus size: 83
11047 CATAAAATGT
* * ** *
11057 TGTATCGATACAATGTATCGATACATATTTTTTTGTATCGATACAATTTAAGCTATTGCCAAAAA
1 TGTATCGATACATTGTATCGATACATA-TTCTTTGTATCGATACAATGCAAGCAATTGCC--AAA
*
11122 ATGTATCGATACATTACTCAAA
63 ATGTATCGATACATT-CTAAAA
* * *
11144 TGTATCGATACATTGTATCGATACACTGA-TCTTTGTATCGATAC-ATGCAGGCAATTTGCCCAG
1 TGTATCGATACATTGTATCGATACA-T-ATTCTTTGTATCGATACAATGCAAGCAA-TTGCCAAA
*
11207 ATGTATCGATACATTTTAAAA
63 ATGTATCGATACATTCTAAAA
11228 TGTATCGATACAT
1 TGTATCGATACAT
11241 GCAGGCAAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
84 17 0.20
85 16 0.19
86 6 0.07
87 43 0.51
88 1 0.01
89 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (83 bp):
TGTATCGATACATTGTATCGATACATATTCTTTGTATCGATACAATGCAAGCAATTGCCAAAATG
TATCGATACATTCTAAAA
Found at i:11271 original size:52 final size:52
Alignment explanation
Indices: 11177--11304 Score: 206
Period size: 52 Copynumber: 2.5 Consensus size: 52
11167 CACTGATCTT
* *
11177 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATT-AAA
11228 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATTAAA
*
11280 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
11305 TCATATTTCG
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 19 0.26
52 50 0.69
53 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATTAAA
Done.