Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3821
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: 14652
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.32
Found at i:2068 original size:22 final size:22
Alignment explanation
Indices: 2043--2117 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
2033 TTTCACATTC
2043 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * * *
2065 ATCACACAT-ACACATTTC-ACATT
1 ATCACA-TTGGC-CA-TTCGGCCTT
2088 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
2111 ATCACAT
1 ATCACAT
2118 ATATATACAC
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
22 17 0.44
23 12 0.31
24 10 0.26
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:2151 original size:49 final size:47
Alignment explanation
Indices: 1832--2232 Score: 559
Period size: 46 Copynumber: 8.6 Consensus size: 47
1822 GCCTTCGGGA
* * *
1832 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1879 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTC-GC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
1925 CTTATCTCATATAT--A-TGTTCACATTCATCACATT-GCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
1969 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTTCAGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCA-TTCGGC
*
2017 CTTATCTCATATAT-CA-TTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
2062 CTTATCACACATACACA-TTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
2108 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
2157 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATTGGCCATTCGGC
*
2206 CTTATCACACATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
2233 TATTCAAAAT
Statistics
Matches: 323, Mismatches: 19, Indels: 24
0.88 0.05 0.07
Matches are distributed among these distances:
43 8 0.02
44 31 0.10
45 16 0.05
46 96 0.30
47 67 0.21
48 23 0.07
49 82 0.25
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:3612 original size:85 final size:85
Alignment explanation
Indices: 3483--3661 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
3473 TATTTTATTG
*
3483 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
3548 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
3568 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
3633 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
3653 CCCATGCTC
1 CCCATGCTC
3662 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:4984 original size:39 final size:40
Alignment explanation
Indices: 4902--5250 Score: 514
Period size: 40 Copynumber: 8.9 Consensus size: 40
4892 ACACGTCACC
* * * * *
4902 GCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCA
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
* ** * *
4942 GCACGAATGCTCTTCGGGGTTTAGCAC-GATATATCACTA
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
* *
4981 GCACGAATGCTCTTCGGAACTTAG-CCGGATACATCACTA
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
5020 GCATGAATGCTCTTCGGGACTTAG-CCGGATACATCACTA
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
5059 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
* * *
5099 GCACGAATGCTCTTCGGAACTTAACCCGGATACATCACTA
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
5139 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
5179 GCATGAATGCTCTTC--GACTTAGCCCGGATACATCACTA
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
5217 GCATGAATGCTCTTC-GGACTTAGCCCGGAT-CATC
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATC
5251 GTCGAGACCT
Statistics
Matches: 285, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
38 43 0.15
39 117 0.41
40 125 0.44
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTA
Found at i:5044 original size:78 final size:80
Alignment explanation
Indices: 4902--5250 Score: 514
Period size: 78 Copynumber: 4.5 Consensus size: 80
4892 ACACGTCACC
* * * * * **
4902 GCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGC
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGC
* *
4967 AC-GATATATCACTA
66 CCGGATACATCACTA
* * *
4981 GCACGAATGCTCTTCGGAACTTAG-CCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAG-
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGC
5044 CCGGATACATCACTA
66 CCGGATACATCACTA
* *
5059 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAAC
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGC
5124 CCGGATACATCACTA
66 CCGGATACATCACTA
*
5139 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTC--GACTTAGC
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGC
5202 CCGGATACATCACTA
66 CCGGATACATCACTA
5217 GCATGAATGCTCTTC-GGACTTAGCCCGGAT-CATC
1 GCATGAATGCTCTTCGGGACTTAGCCCGGATACATC
5251 GTCGAGACCT
Statistics
Matches: 247, Mismatches: 20, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
76 4 0.02
77 16 0.06
78 102 0.41
79 56 0.23
80 69 0.28
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
GCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGC
CCGGATACATCACTA
Found at i:5350 original size:38 final size:38
Alignment explanation
Indices: 5302--5376 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
5292 CAATTTTAAT
*
5302 CCGGACATAATCTCTGT-ACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCT-TCACATAGCCAGCGGGTCTTTAC
* *
5340 CCGGACATAATCTCTTCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTA
5377 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTAC
Found at i:8013 original size:47 final size:47
Alignment explanation
Indices: 7816--8359 Score: 828
Period size: 47 Copynumber: 11.8 Consensus size: 47
7806 TTATCACTTC
* *
7816 CACATCCATCACATTGGCCATTCGGCCTTATCACATATA-AC-T-TT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
* * **
7860 CACATTCATCACATTGGCCATT-GGCCTTATCTCATATATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
7906 CACATTCATCACATTGGCCATTCGGCCTTATCACACAT--ACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
7951 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
* * **
7998 CACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
8045 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
* *
8092 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATTACACT-TT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATA-CACA-TGTT
*
8140 CACATTCATCACATTGGCCATTCGG-CTTAT--CACATA-TCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
8183 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACACT-TT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTT
8230 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACAT-TT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
* *
8276 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAT-TT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
8322 CACATTCATCACATTGGCCATTCGGCCTTATCACACAT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACAT
8360 TTCACATTGG
Statistics
Matches: 464, Mismatches: 22, Indels: 26
0.91 0.04 0.05
Matches are distributed among these distances:
42 1 0.00
43 44 0.09
44 27 0.06
45 50 0.11
46 114 0.25
47 196 0.42
48 31 0.07
49 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
Found at i:8264 original size:22 final size:22
Alignment explanation
Indices: 8237--8356 Score: 75
Period size: 22 Copynumber: 5.3 Consensus size: 22
8227 TTTCACATTC
8237 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * * *
8259 ATCACACAT-ACACATTTC-ACATT
1 ATCACA-TTGGC-CA-TTCGGCCTT
8282 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
*** * *
8305 ATCACATATATACATTTC-ACATT
1 ATCACAT-TGGCCA-TTCGGCCTT
8328 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
8351 ATCACA
1 ATCACA
8357 CATTTCACAT
Statistics
Matches: 70, Mismatches: 18, Indels: 20
0.65 0.17 0.19
Matches are distributed among these distances:
22 26 0.37
23 24 0.34
24 20 0.29
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:8356 original size:77 final size:78
Alignment explanation
Indices: 8275--8435 Score: 274
Period size: 77 Copynumber: 2.1 Consensus size: 78
8265 CATACACATT
8275 TCACATTCA-TCACATTGGCCATTCGGCCTTATCACATATATACA-TTTCACATTCATCACATTG
1 TCACA-TCATTCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTG
*
8338 GCCATTCGGCCTTA
65 GCCATTAGGCCTTA
8352 TCACA-CATTTCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTG
1 TCACATCA-TTCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTG
8416 GCCATTAGGCCTTA
65 GCCATTAGGCCTTA
8430 TCACAT
1 TCACAT
8436 ATATATACAC
Statistics
Matches: 79, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
75 2 0.03
77 40 0.51
78 37 0.47
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.34
Consensus pattern (78 bp):
TCACATCATTCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTGG
CCATTAGGCCTTA
Found at i:8406 original size:31 final size:31
Alignment explanation
Indices: 8322--8396 Score: 105
Period size: 31 Copynumber: 2.3 Consensus size: 31
8312 ATATACATTT
8322 CACATTCATCACATTGGCCATTCGGCCTTATCA
1 CACATT-A-CACATTGGCCATTCGGCCTTATCA
*
8355 CACATTTCACATTGGCCATTCGGCCTTATCA
1 CACATTACACATTGGCCATTCGGCCTTATCA
*
8386 CATATATACAC
1 CACAT-TACAC
8397 TTTCACATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 28 0.74
32 4 0.11
33 6 0.16
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.31
Consensus pattern (31 bp):
CACATTACACATTGGCCATTCGGCCTTATCA
Found at i:8412 original size:308 final size:315
Alignment explanation
Indices: 7796--8549 Score: 1072
Period size: 324 Copynumber: 2.4 Consensus size: 315
7786 CCCTTCGGGA
* * * *
7796 CTTATCACATTTA-T-CACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATAACTT
1 CTTATCACATATATTACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATCACTT
* *
7859 TCACATTCATCACATTGGCCATTGGCCTTATCTCATATATGCA-TGTTCACATTCATCACATTGG
66 TCACATTCATCACATTGGCCATTGGCCTTATCACATATATACACT-TTCACATTCATCACATTGG
7923 CCATTCGGCCTTATCACACATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACA
130 CCATTCGGCCTTATCACACATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACA
7988 TACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCA
195 TACACATGTTCACATTCATCACATTGGCCATTCGG-----TCTCATATATGCA---TCACATT-A
*
8053 TCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
251 TCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTAGGC
8118 CTTATCACATATATTACACTTTCACATTCATCACATTGGCCATTCGG-CTTATCACATATCA-TG
1 CTTATCACATATATTACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATCACT-
* *
8181 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACACTTTCACATTCATCACATTG
65 TTCACATTCATCACATTGGCCATT-GGCCTTATCACATATATACACTTTCACATTCATCACATTG
8246 GCCATTCGGCCTTATCACACATACACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC
129 GCCATTCGGCCTTATCACACAT--ACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
* *
8310 ATATATACAT-TTCACATTCATCACATTGGCCATTCGG-C-C-T-TAT-CA-CACATT-TCACAT
192 ACATACACATGTTCACATTCATCACATTGGCCATTCGGTCTCATATATGCATCACATTATCACAT
* *
8367 TGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTAGGC
257 TGGCCATTCGGCCTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTAGGC
*
8426 CTTATCACATATATATACACTTTCACATTCATCACA-TGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATAT-TACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC----ATAT
8490 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATT
61 -CACTTTCACATTCATCACATTGGCCATT-GGCCTTATCACATATATACACTTTCACATT
8550 TATTCAAATA
Statistics
Matches: 399, Mismatches: 17, Indels: 40
0.88 0.04 0.09
Matches are distributed among these distances:
308 84 0.21
309 30 0.08
310 6 0.02
313 4 0.01
314 56 0.14
315 4 0.01
316 1 0.00
317 1 0.00
318 1 0.00
322 13 0.03
323 38 0.10
324 112 0.28
325 45 0.11
326 4 0.01
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (315 bp):
CTTATCACATATATTACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATCACTT
TCACATTCATCACATTGGCCATTGGCCTTATCACATATATACACTTTCACATTCATCACATTGGC
CATTCGGCCTTATCACACATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACAT
ACACATGTTCACATTCATCACATTGGCCATTCGGTCTCATATATGCATCACATTATCACATTGGC
CATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTAGGC
Found at i:8459 original size:49 final size:47
Alignment explanation
Indices: 8361--8549 Score: 326
Period size: 48 Copynumber: 4.0 Consensus size: 47
8351 ATCACACATT
*
8361 TCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCA
1 TCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCA
8408 TCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATTGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCA
8457 TCACA-TGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATTGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCA
8505 TCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATT
1 TCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATT
8550 TATTCAAATA
Statistics
Matches: 138, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
47 44 0.32
48 48 0.35
49 46 0.33
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCA
Found at i:8483 original size:124 final size:122
Alignment explanation
Indices: 8229--8483 Score: 397
Period size: 124 Copynumber: 2.0 Consensus size: 122
8219 ATACACACTT
8229 TCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATTTCACATTCATCACATTGGC
1 TCACATT-ATCACATTGGCCATTCGGCCTTATCACACATACACATTTCACATTCATCACATTGGC
* *
8294 CATTCGGCCTTATCACATATATACATTTCACATTCATCACATTGGCCATTCGGCCTTA
65 CATTAGGCCTTATCACATATATACATTTCACATTCATCACATTGGCCATTAGGCCTTA
* *
8352 TCACACATT-TCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTG
1 T--CACATTATCACATTGGCCATTCGGCCTTATCACACATACACA-TTTCACATTCATCACATTG
8416 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA-TGGCCATTAGGCCTTA
63 GCCATTAGGCCTTATCAC--ATATATACA-TTTCACATTCATCACATTGGCCATTAGGCCTTA
8478 TCACAT
1 TCACAT
8484 ATATATACAC
Statistics
Matches: 122, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
123 34 0.28
124 41 0.34
125 6 0.05
126 25 0.20
127 16 0.13
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (122 bp):
TCACATTATCACATTGGCCATTCGGCCTTATCACACATACACATTTCACATTCATCACATTGGCC
ATTAGGCCTTATCACATATATACATTTCACATTCATCACATTGGCCATTAGGCCTTA
Found at i:8517 original size:97 final size:94
Alignment explanation
Indices: 8361--8549 Score: 326
Period size: 97 Copynumber: 2.0 Consensus size: 94
8351 ATCACACATT
*
8361 TCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 TCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
8426 CTTATCACATATATATACACTTTCACATTCA
66 CTTATCAC--ATATATACACTTTCACATTCA
8457 TCACA-TGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAG
1 TCACATTGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAG
8521 GCCTTATCACATATATACACTTTCACATT
64 GCCTTATCACATATATACACTTTCACATT
8550 TATTCAAATA
Statistics
Matches: 90, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
95 38 0.42
96 5 0.06
97 47 0.52
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (94 bp):
TCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
CTTATCACATATATACACTTTCACATTCA
Found at i:9940 original size:85 final size:85
Alignment explanation
Indices: 9811--9989 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
9801 TATTTTATTG
*
9811 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
9876 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
9896 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
9961 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
9981 CCCATGCTC
1 CCCATGCTC
9990 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:11383 original size:40 final size:40
Alignment explanation
Indices: 11233--11587 Score: 535
Period size: 40 Copynumber: 9.1 Consensus size: 40
11223 CGAATACACG
* * * *
11233 TCACCAGCATGATTGCTCTTC-GGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * * * *
11272 ACACCAGCACGAATGCTCTTCGGG-TTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
11311 TCACTAGCACGAATGCT-TTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
11350 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
11390 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
11430 TCACTAGCACGAATGCTCTTCGGAACTTA-CCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
11469 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
11509 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
11549 TCACTAGCA-GAATGCTCTTC-GGACTTAGCCCGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
11586 TC
1 TC
11588 GTCGAGACCT
Statistics
Matches: 294, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
37 4 0.01
38 20 0.07
39 121 0.41
40 149 0.51
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:11404 original size:79 final size:79
Alignment explanation
Indices: 11233--11587 Score: 531
Period size: 79 Copynumber: 4.5 Consensus size: 79
11223 CGAATACACG
* * * * * * *
11233 TCACCAGCATGATTGCTCTTCGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGG-T
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
* *
11297 TTAGCACGGATATA
66 TTAGCCCGGATACA
* *
11311 TCACTAGCACGAATGCT-TTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
11375 CTTAGCCCGGATACA
65 CTTAGCCCGGATACA
*
11390 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAA
1 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
11455 CTTA-CCCGGATACA
65 CTTAGCCCGGATACA
*
11469 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
11534 CTTAGCCCGGATACA
65 CTTAGCCCGGATACA
11549 TCACTAGCA-GAATGCTCTTCGGACTTAGCCCGGAT-CATC
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACATC
11588 GTCGAGACCT
Statistics
Matches: 256, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
77 9 0.04
78 64 0.25
79 116 0.45
80 65 0.25
81 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
TTAGCCCGGATACA
Found at i:11433 original size:119 final size:120
Alignment explanation
Indices: 11233--11587 Score: 571
Period size: 119 Copynumber: 3.0 Consensus size: 120
11223 CGAATACACG
* * * * * * *
11233 TCACCAGCATGATTGCTCTTC-GGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGG-
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
* * *
11296 TTTAGCACGGATATATCACTAGCACGAATGCT-TTCGGAACTTAGCCCGGATACA
66 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
11350 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
11415 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTA-CCCGGATACA
66 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
11469 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
11534 CTTAGCCCGGATACATCACTAGCA-GAATGCTCTTCGG-ACTTAGCCCGGAT-CA
66 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
11586 TC
1 TC
11588 GTCGAGACCT
Statistics
Matches: 224, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
117 28 0.12
118 57 0.25
119 128 0.57
120 11 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (120 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:14193 original size:47 final size:47
Alignment explanation
Indices: 14130--14373 Score: 375
Period size: 47 Copynumber: 5.2 Consensus size: 47
14120 CCCTTCGGGA
* * *
14130 CTTATCACATTTATACACT-TCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
14177 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* *
14224 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
14271 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
14318 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
14365 CTTATCACA
1 CTTATCACA
14374 CATGTTGGCC
Statistics
Matches: 187, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 1 0.01
47 186 0.99
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:14392 original size:73 final size:74
Alignment explanation
Indices: 14305--14448 Score: 238
Period size: 75 Copynumber: 1.9 Consensus size: 74
14295 ATTCATCACA
*
14305 TTGGCCATTCGGCCTTATCAC-ACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTT
1 TTGGCCATTCGGCCTTATCACAACATACACACT-TTCACATTCATCACATTGGCCATTAGGCCTT
14368 ATCACACATG
65 ATCACACATG
*
14378 TTGGCCATTCGGCCTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTAGGCCTT
1 TTGGCCATTCGGCCTTATCACA-ACATACACACTTTCACATTCATCACATTGGCCATTAGGCCTT
14443 ATCACA
65 ATCACA
14449 TATACACTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
73 21 0.32
75 44 0.67
76 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (74 bp):
TTGGCCATTCGGCCTTATCACAACATACACACTTTCACATTCATCACATTGGCCATTAGGCCTTA
TCACACATG
Done.