Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold900
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: 8766
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:1277 original size:35 final size:35
Alignment explanation
Indices: 1231--1344 Score: 163
Period size: 35 Copynumber: 3.5 Consensus size: 35
1221 ATGCCTTCAA
1231 TTTTATTCCATGCCCATCATATTATGCCTTCATTT
1 TTTTATTCCATGCCCATCATATTATGCCTTCATTT
1266 TTTTATTCCATG-CC--C-----ATGCCTTCATTT
1 TTTTATTCCATGCCCATCATATTATGCCTTCATTT
*
1293 TTATATTCCATGCCCATCATATTATGCCTTCATTT
1 TTTTATTCCATGCCCATCATATTATGCCTTCATTT
1328 TTTTATTCCATGCCCAT
1 TTTTATTCCATGCCCAT
1345 GCCTTCATTT
Statistics
Matches: 69, Mismatches: 2, Indels: 16
0.79 0.02 0.18
Matches are distributed among these distances:
27 23 0.33
28 2 0.03
30 1 0.01
32 1 0.01
34 2 0.03
35 40 0.58
ACGTcount: A:0.19, C:0.27, G:0.06, T:0.47
Consensus pattern (35 bp):
TTTTATTCCATGCCCATCATATTATGCCTTCATTT
Found at i:1284 original size:27 final size:27
Alignment explanation
Indices: 1254--1370 Score: 137
Period size: 27 Copynumber: 4.1 Consensus size: 27
1244 CCATCATATT
*
1254 ATGCCTTCATTTTTTTATTCCATGCCC
1 ATGCCTTCATTTTTATATTCCATGCCC
1281 ATGCCTTCATTTTTATATTCCATGCCCATC
1 ATGCCTTCATTTTTATATTCCATG-CC--C
*
1311 ATATTATGCCTTCATTTTTTTATTCCATGCCC
1 -----ATGCCTTCATTTTTATATTCCATGCCC
1343 ATGCCTTCA-TTTTATATTCCATGCCC
1 ATGCCTTCATTTTTATATTCCATGCCC
1369 AT
1 AT
1371 CATTCCGTGT
Statistics
Matches: 79, Mismatches: 3, Indels: 17
0.80 0.03 0.17
Matches are distributed among these distances:
26 18 0.23
27 32 0.41
28 2 0.03
30 1 0.01
32 1 0.01
34 2 0.03
35 23 0.29
ACGTcount: A:0.19, C:0.28, G:0.07, T:0.46
Consensus pattern (27 bp):
ATGCCTTCATTTTTATATTCCATGCCC
Found at i:1303 original size:21 final size:21
Alignment explanation
Indices: 1279--1341 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
1269 TATTCCATGC
1279 CCATGCCTTCATTTTTATATT
1 CCATGCCTTCATTTTTATATT
*
1300 CCATGCC--CA---TCATATT
1 CCATGCCTTCATTTTTATATT
*
1316 --ATGCCTTCATTTTTTTATT
1 CCATGCCTTCATTTTTATATT
1335 CCATGCC
1 CCATGCC
1342 CATGCCTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
14 5 0.16
16 8 0.25
19 7 0.22
21 12 0.38
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (21 bp):
CCATGCCTTCATTTTTATATT
Found at i:1307 original size:62 final size:61
Alignment explanation
Indices: 1219--1373 Score: 285
Period size: 62 Copynumber: 2.5 Consensus size: 61
1209 ATCCATCATT
*
1219 CCATGCCTTCAATTT-TATTCCATGCCCATCATATTATGCCTTCATTTTTTTATTCCATGC
1 CCATGCCTTCATTTTATATTCCATGCCCATCATATTATGCCTTCATTTTTTTATTCCATGC
1279 CCATGCCTTCATTTTTATATTCCATGCCCATCATATTATGCCTTCATTTTTTTATTCCATGC
1 CCATGCCTTCA-TTTTATATTCCATGCCCATCATATTATGCCTTCATTTTTTTATTCCATGC
1341 CCATGCCTTCATTTTATATTCCATGCCCATCAT
1 CCATGCCTTCATTTTATATTCCATGCCCATCAT
1374 TCCGTGTTTT
Statistics
Matches: 92, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
60 11 0.12
61 25 0.27
62 56 0.61
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.45
Consensus pattern (61 bp):
CCATGCCTTCATTTTATATTCCATGCCCATCATATTATGCCTTCATTTTTTTATTCCATGC
Found at i:1355 original size:26 final size:27
Alignment explanation
Indices: 1316--1370 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 27
1306 CCATCATATT
*
1316 ATGCCTTCATTTTTTTATTCCATGCCC
1 ATGCCTTCATTTTTATATTCCATGCCC
1343 ATGCCTTCA-TTTTATATTCCATGCCC
1 ATGCCTTCATTTTTATATTCCATGCCC
1369 AT
1 AT
1371 CATTCCGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.18, C:0.29, G:0.07, T:0.45
Consensus pattern (27 bp):
ATGCCTTCATTTTTATATTCCATGCCC
Found at i:2574 original size:7 final size:7
Alignment explanation
Indices: 2533--2568 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
2523 AACAAAAAAT
2533 AAATAAA
1 AAATAAA
2540 AAATAAA
1 AAATAAA
2547 AAATAAA
1 AAATAAA
2554 AAATGAAA
1 AAAT-AAA
2562 AAA-AAA
1 AAATAAA
2568 A
1 A
2569 GAAAAAGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 4 0.14
7 18 0.64
8 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (7 bp):
AAATAAA
Found at i:3654 original size:61 final size:61
Alignment explanation
Indices: 3494--3834 Score: 386
Period size: 61 Copynumber: 5.6 Consensus size: 61
3484 ACATGACAAC
* * *
3494 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATACCT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGA-AGCT
* * * * * ** *
3556 TTTTCCTTTCAAAGCCCACATAAATTTGTGGTACCTTTTGGTCCTCAAAGAGTAGGACG-T
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGAAGCT
* * *
3616 ATTTCCCTTTTAAAGTCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAAGAAGCT
1 -TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGAAGCT
* * *
3678 TTTTCCTTTTAAAGCCCACGCAAGTTGGTGGCACCTTTCAGTCCTTAAAAAAG-AGGAAGCT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC-TCAAAGAGTAGGAAGCT
* * * *
3739 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAAAATA-GAA-CAC
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGAAGC-T
* * * *
3799 TTTT-GTTTCAAAGCCCACACAAGTTGTTAGCACCTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
3835 CAAGACGTCC
Statistics
Matches: 237, Mismatches: 37, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
59 29 0.12
60 14 0.06
61 139 0.59
62 55 0.23
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (61 bp):
TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGAAGCT
Found at i:3758 original size:122 final size:123
Alignment explanation
Indices: 3494--4224 Score: 479
Period size: 122 Copynumber: 6.2 Consensus size: 123
3484 ACATGACAAC
* *
3494 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATACCTTTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGATACCTTTT
* * * ** * * *
3559 TCCTTTCAAAGCCCACATAAATTTGTGGTACCTTTTGGTCCTCAAAGAGTAGGACGTA
66 TCCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTCCTAAAAAAGTAGGAAGTA
* * * *
3617 TTTCCCTTTTAAAGTCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAAGA-AGCTTTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGATACCTTTT
* * *
3681 TCCTTTTAAAGCCCACGCAAGTTGGTGGCACCTTTCAGTCCTTAAAAAAG-AGGAAGCT-
66 TCCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTCC-TAAAAAAGTAGGAAG-TA
* *
3739 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAA-A-AATAGA-ACAC-T
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCA-AGATAC-CTT
* * * * * *
3800 TTT-GTTTCAAAGCCCACACAAGTTGTTAGCACC--T---T-C------A--A-GACGTC
64 TTTCCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTCCTAAAAAAGTAGGAAGTA
* * * *
3844 CTTCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTAAAAGAGCAAGAT-GCTTTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGATACCTTTT
* * * * * * * * * *
3908 TTCTTTTAAAGCCCCCACAAGTTGGTGGCACCTTTCCGTTCTCAAAAAGCAAG-A-CA
66 TCCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTCCTAAAAAAGTAGGAAGTA
* ** * * * *
3964 CTTTCCTTTCGAAG-CC-CACAAGTTAGTGGCACCTTTTAGTCCTCAAAGAGC-AG-GACGTTTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGATACCTTTT
* * * * * * ** * * **
4025 CCCTTTCAAAGCCCACGCAAGTTGGTGGCACCTTTTAGTCTTCAAGGAGCAGGATGCC
66 TCCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTCCTAAAAAAGTAGGAAGTA
* ** * * *
4083 CTTTCCTTTTAAAGCTTACACAAG-TGGTGGCACCTTTTTAGTCCTCAAAGAGCAGGACA-C--T
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTCAGTCCTCAAAGAGCAAGATACCTTT
* * * ** * * * * * * *
4144 TTCCTTTAAAAGCCCACATAAGTTAATGACACCTTTTAGTCCTTAAAGAGCAAGACGTA
65 TTCCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTCCTAAAAAAGTAGGAAGTA
*
4203 -TTTCCTTTTCAAGCCCACACAA
1 TTTTCCTTTTAAAGCCCACACAA
4225 ACTAGTGACT
Statistics
Matches: 485, Mismatches: 90, Indels: 70
0.75 0.14 0.11
Matches are distributed among these distances:
104 1 0.00
105 49 0.10
106 9 0.02
107 27 0.06
109 1 0.00
112 1 0.00
113 1 0.00
114 1 0.00
115 1 0.00
117 47 0.10
118 33 0.07
119 35 0.07
120 92 0.19
121 34 0.07
122 93 0.19
123 60 0.12
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (123 bp):
TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGATACCTTTT
TCCTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTCCTAAAAAAGTAGGAAGTA
Found at i:3967 original size:166 final size:166
Alignment explanation
Indices: 3682--3983 Score: 466
Period size: 166 Copynumber: 1.8 Consensus size: 166
3672 GAAGCTTTTT
* *
3682 CCTTTTAAAGCCCACGCAAGTTGGTGGCACCTTTCAGTCCTTAAAAAAGAGGAAGCTTTTTCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTTAAAAAAGAAGAAGCTTTTTCCTT
**
3747 TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAAAATAGAACACTTTTGTTTCAAAG
66 TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAAAATAGAACACTTTCCTTTCAAAG
3812 CCCACACAAGTTGTTAGCACCTTCAAGACGTCCTTC
131 CCCACACAAGTTGTTAGCACCTTCAAGACGTCCTTC
* * *
3848 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC-TAAAAGAGCAAGATGCTTTTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTTAAAAAAG-AAGAAGCTTTTTCCT
* * *
3912 TTTAAAGCCCCCACAAGTTGGTGGCACCTTTCCGTTCTCAAAAAGCA-AG-ACACTTTCCTTTCG
65 TTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAAA--ATAGAACACTTTCCTTTCA
3975 AAGCCCACA
128 AAGCCCACA
3984 AGTTAGTGGC
Statistics
Matches: 123, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
165 7 0.06
166 113 0.92
167 2 0.02
168 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (166 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTTAAAAAAGAAGAAGCTTTTTCCTT
TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAAAATAGAACACTTTCCTTTCAAAG
CCCACACAAGTTGTTAGCACCTTCAAGACGTCCTTC
Found at i:4056 original size:60 final size:59
Alignment explanation
Indices: 3848--4224 Score: 357
Period size: 61 Copynumber: 6.3 Consensus size: 59
3838 GACGTCCTTC
* * * *
3848 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTAAAAGAGCAAGATGCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGC--TTT
* * * ** * * *
3909 TCTTTTAAAGCCCCCACAAGTTGGTGGCACCTTTCCGTTCTCAAAAAGCAAGACACTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCTTT
* * * *
3968 CCTTTCGAAG-CC-CACAAGTTAGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCTTT
* * * * *
4025 CCCTTTCAAAGCCCACGCAAGTTGGTGGCACCTTTTAGTCTTCAAGGAGCAGGATGCCCTTT
1 -CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGA--CGCTTT
* ** * *
4087 CCTTTTAAAGCTTACACAAG-TGGTGGCACCTTTTTAGTCCTCAAAGAGCAGGACACTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTTTAGTCCTCAAAGAGCAAGACGCTTT
* * ** * * *
4146 CCTTTAAAAGCCCACATAAGTTAATGACACCTTTTAGTCCTTAAAGAGCAAGACGTATTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACG-CTTT
4206 CCTTTTC-AAGCCCACACAA
1 CC-TTTCAAAGCCCACACAA
4225 ACTAGTGACT
Statistics
Matches: 261, Mismatches: 46, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
57 37 0.14
58 11 0.04
59 54 0.21
60 68 0.26
61 87 0.33
62 4 0.02
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (59 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCTTT
Found at i:4144 original size:178 final size:180
Alignment explanation
Indices: 3835--4224 Score: 491
Period size: 178 Copynumber: 2.2 Consensus size: 180
3825 TTAGCACCTT
** *
3835 CAAGACGTCCTTCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTAAAAGAGCAAG
1 CAAGACGTATTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTAAAAGAGCAAG
** * * * *
3900 ATGCTTTTTTCTTTTAAAGCCCCCACAAGTTGGTGGCACCTTTCCGTTCTCAAAAAGCAAGACAC
66 ATGCCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGCAAGACAC
** * *
3965 TTTCCTTTCGAAGCCCAC-AAGTTAGTGGCACCTTTTAGTCCTCAAAGAG
131 TTTCCTTTAAAAGCCCACAAAGTTAATGACACCTTTTAGTCCTCAAAGAG
* * * * * * *
4014 CAGGACGT-TTTCCCTTTCAAAGCCCACGCAAGTTGGTGGCACCTTTTAGTCTTCAAGGAGCAGG
1 CAAGACGTATTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTAAAAGAGCAAG
** * * *
4078 ATGCCCTTTCCTTTTAAAGCTTACACAAG-TGGTGGCACCTTTTTAGTCCTCAAAGAGCAGGACA
66 ATGCCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTCAGTCCTCAAAAAGCAAGACA
*
4142 CTTTCCTTTAAAAGCCCACATAAGTTAATGACACCTTTTAGTCCTTAAAGAG
130 CTTTCCTTTAAAAGCCCACA-AAGTTAATGACACCTTTTAGTCCTCAAAGAG
*
4194 CAAGACGTATTTCCTTTTC-AAGCCCACACAA
1 CAAGACGTATTTCCCTTTCAAAGCCCACACAA
4225 ACTAGTGACT
Statistics
Matches: 179, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
177 10 0.06
178 107 0.60
179 7 0.04
180 46 0.26
181 9 0.05
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (180 bp):
CAAGACGTATTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTAAAAGAGCAAG
ATGCCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGCAAGACAC
TTTCCTTTAAAAGCCCACAAAGTTAATGACACCTTTTAGTCCTCAAAGAG
Found at i:4537 original size:52 final size:52
Alignment explanation
Indices: 4388--4538 Score: 128
Period size: 52 Copynumber: 2.9 Consensus size: 52
4378 TTTCACAATT
* * * * * *
4388 TGTATCAATACATTCT-TCAATGTATCTATATATTCTAGGTTTTATTTACCCAGA
1 TGTATCGATACATTTTCTCATTGTATCGATAAATTC-AGG-ATT-TTTACCCAGA
* * * *
4442 TGTATTGATACATTTTTTCATTGTATTGATAAATTCTGGATTTTTACCCAGA
1 TGTATCGATACATTTTCTCATTGTATCGATAAATTCAGGATTTTTACCCAGA
* *
4494 TGTATCGATACCA-TTTCTCA-TGTATCGATACATTCAAGTATTTTT
1 TGTATCGATA-CATTTTCTCATTGTATCGATAAATTC-AGGATTTTT
4539 TACCATTTTG
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
51 13 0.16
52 32 0.41
53 4 0.05
54 15 0.19
55 15 0.19
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (52 bp):
TGTATCGATACATTTTCTCATTGTATCGATAAATTCAGGATTTTTACCCAGA
Found at i:7166 original size:158 final size:159
Alignment explanation
Indices: 6875--7237 Score: 416
Period size: 158 Copynumber: 2.3 Consensus size: 159
6865 TCATTGATGT
* * * * * **
6875 TTTTATTTCTAAAATACCGATTTTCCACCATCGAGGATACTCCAA-CCCCGTTATTTCTGAGGGG
1 TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAACCCCCGTTATTTCCGAGCAG
* * * * *
6939 ATACTCCAACTCCGATTTTATTTCTAAAACACTGATTTTTCACCATCAGGGATACTCCAATCCCG
66 ATACTCCAACTCCGATTTTATTTCTAAAACACTGATTTTCCACAATCAAGAATACTCCAATCCCA
7004 TTATTTTCAAAGGGATACTCCAACCTCGA-
131 TTATTTTCAAAGGGATACTCCAACC-CGAG
** * *
7033 TTTTATTTCCAAAACATTGATTTTTCACAATCGGGGATACTCTAACCCCCGTTATTTCCG-GCAG
1 TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAACCCCCGTTATTTCCGAGCAG
* *
7097 ATACTTCAA-TCCCGATTTTATTT-TCAAAACA-TCGATTTTCCACAATCAAGAATACTCTAA-C
66 ATACTCCAACT-CCGATTTTATTTCT-AAAACACT-GATTTTCCACAATCAAGAATACTCCAATC
** * *
7158 CTCATTATTTTTTAGGGGATACTCCAACCCTAG
128 C-CATTATTTTCAAAGGGATACTCCAACCCGAG
* *
7191 TTTTACTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACC
1 TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAACC
7238 TCGGTTTTAT
Statistics
Matches: 171, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
157 7 0.04
158 151 0.88
159 13 0.08
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (159 bp):
TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAACCCCCGTTATTTCCGAGCAG
ATACTCCAACTCCGATTTTATTTCTAAAACACTGATTTTCCACAATCAAGAATACTCCAATCCCA
TTATTTTCAAAGGGATACTCCAACCCGAG
Found at i:7235 original size:51 final size:52
Alignment explanation
Indices: 7172--7289 Score: 161
Period size: 51 Copynumber: 2.3 Consensus size: 52
7162 TTATTTTTTA
7172 GGGGATACTCCAACCCT-AGTTTTACTTCCAAAACACC-AATTTTCCACAATC
1 GGGGATACTCCAACCCTCAGTTTTACTTCCAAAACACCGAATTTTCC-CAATC
* * ** *
7223 GGGGATACTCCAA-CCTCGGTTTTATTTTTAAAACACCGATTTTTCCCAATC
1 GGGGATACTCCAACCCTCAGTTTTACTTCCAAAACACCGAATTTTCCCAATC
7274 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
7290 CATTAATTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
50 3 0.05
51 47 0.80
52 9 0.15
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.29
Consensus pattern (52 bp):
GGGGATACTCCAACCCTCAGTTTTACTTCCAAAACACCGAATTTTCCCAATC
Found at i:7239 original size:79 final size:78
Alignment explanation
Indices: 6875--7237 Score: 352
Period size: 79 Copynumber: 4.6 Consensus size: 78
6865 TCATTGATGT
* * * * * *
6875 TTTTATTTCTAAAATACCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAGGGGA
1 TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
6940 TACTCCAACTCCGA
66 TACTCCAAC-CCGA
* * * * * * * *
6954 TTTTATTTCTAAAACACTGATTTTTCACCATCAGGGATACTCCAATCCCGTTATTTTCAAAGGGA
1 TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
7019 TACTCCAACCTCGA
66 TACTCCAACC-CGA
** * * ** *
7033 TTTTATTTCCAAAACATTGATTTTTCACAATCGGGGATACTCTAACCCCCGTTA--TTTCCGGCA
1 TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAA-CCCCGTTATTTTTAAGG-G
*
7096 GATACTTCAATCCCGA
64 GATACTCCAA-CCCGA
* * ** * * * * *
7112 TTTTATTTTCAAAACATCGATTTTCCACAATCAAGAATACTCTAACCTCATTATTTTTTAGGGGA
1 TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
*
7177 TACTCCAACCCTA
66 TACTCCAACCCGA
* *
7190 GTTTTACTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACC
1 -TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAACC
7238 TCGGTTTTAT
Statistics
Matches: 234, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
78 14 0.06
79 206 0.88
80 14 0.06
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (78 bp):
TTTTATTTCCAAAACACCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
TACTCCAACCCGA
Found at i:7435 original size:127 final size:128
Alignment explanation
Indices: 7113--7461 Score: 344
Period size: 130 Copynumber: 2.7 Consensus size: 128
7103 CAATCCCGAT
* * * * * * * ***
7113 TTTATTTTCAAAACATCGATTTTCCACAATC-AAGAATACTCTAACCTCATTATTTTTTAGGGGA
1 TTTATTTTTAAAACACCGATTTTTCACAATCGGAG-ATACTCCAACCCCATTAATTCCAAGGGGA
* **
7177 TACTCCAACCCTAGTTTTACTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGG
65 TACTCCAACCC-AGTTTTATTTCCAAAACACCAATTTTCCACAATCAAGGATACTCCAACCTC-G
*
7242 T
128 C
* * *** *
7243 TTTATTTTTAAAACACCGATTTTTCCCAATCGGGGATACTCCAACCCCATTAATTCTGCGAGGAT
1 TTTATTTTTAAAACACCGATTTTTCACAATCGGAGATACTCCAACCCCATTAATTCCAAGGGGAT
*** ** *
7308 ACTCCAACCTCAGTTTTATTTCCAAAACATTGATTTTTTACAATCAAGGATGCTCCAACC-C-C
66 ACTCCAACC-CAGTTTTATTTCCAAAACACCAATTTTCCACAATCAAGGATACTCCAACCTCGC
* * * *
7370 TTTATTTTTAGAACACCGATTTTTCACAATCGGAGATACTTCGACCCCATTATTTCCAAGGGGAT
1 TTTATTTTTAAAACACCGATTTTTCACAATCGGAGATACTCCAACCCCATTAATTCCAAGGGGAT
* *
7435 ACTCCAACCCCATTTTTATCTCCAAAA
66 ACTCCAA-CCCAGTTTTATTTCCAAAA
7462 TAGTAAATTT
Statistics
Matches: 181, Mismatches: 35, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
127 77 0.43
128 2 0.01
129 1 0.01
130 99 0.55
131 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (128 bp):
TTTATTTTTAAAACACCGATTTTTCACAATCGGAGATACTCCAACCCCATTAATTCCAAGGGGAT
ACTCCAACCCAGTTTTATTTCCAAAACACCAATTTTCCACAATCAAGGATACTCCAACCTCGC
Done.