Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1817
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: 43967
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:886 original size:38 final size:38
Alignment explanation
Indices: 822--1078 Score: 265
Period size: 38 Copynumber: 6.5 Consensus size: 38
812 TTCCGAGGTT
* * *
822 TTAGCTCGGATATAT-TCTAGCACGAAT-CTCTTCGAAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTC-TCGGAC
* *
859 TTAGCCCGGATACATCACTAGCACGAATGCTCTGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTCGGAC
897 TTAGCCCGGATATATCACTAGCACGAATGCTCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTC-GGAC
936 TTAG--CGGATATATCACTTAGCACGAGATGCTCCTCGGAC
1 TTAGCCCGGATATATCAC-TAGCACGA-ATGCT-CTCGGAC
975 TTTAGCCCGGATATTATCACTAGCAGCGGAATGCTGCTCGGAC
1 -TTAGCCCGGATA-TATCACTAGCA-C-GAATGCT-CTCGGAC
1018 TT-GCCCTGGATATATCACGTAGCAC-AATGGCTCCTCGGGAC
1 TTAGCCC-GGATATATCAC-TAGCACGAAT-GCT-CTC-GGAC
* *
1059 TTAGCCAGCATATATTCACT
1 TTAGCCCGGATATA-TCACT
1079 CTCAATTCTC
Statistics
Matches: 191, Mismatches: 11, Indels: 32
0.82 0.05 0.14
Matches are distributed among these distances:
37 25 0.13
38 55 0.29
39 23 0.12
40 13 0.07
41 24 0.13
42 30 0.16
43 19 0.10
44 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (38 bp):
TTAGCCCGGATATATCACTAGCACGAATGCTCTCGGAC
Found at i:3003 original size:47 final size:47
Alignment explanation
Indices: 2450--4187 Score: 1911
Period size: 47 Copynumber: 35.9 Consensus size: 47
2440 TGCCCTTCGA
* * * * * *
2450 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
2497 CCT-T-ACATATATACACTAT-ACATTCATTACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
** *
2541 CTTATCACATAT-TACACTTTCACATTCATCACAT-GGCTCCGTA-GT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGC-CATTAGGC
* *
2586 CTTATCAC--ATATACACGTTCACATTCATCACATCGCCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2631 CTTATTCACATATGATAACACTTTCACATTCATTCACATCGG-CATTAGGC
1 CTTA-TCACATAT-AT-ACACTTTCACATTCA-TCACATCGGCCATTAGGC
2681 CTTATACACATTATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTAT-CACA-TATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2729 CTTATCACATATATATACACTTTCGCATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* **
2778 CCTATACACATATAATACACTTTCACATTCATCACATCGGCCATTATTC
1 CTTAT-CACATAT-ATACACTTTCACATTCATCACATCGGCCATTAGGC
2827 CTTA-CACATATATACACTTTCA-ATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2872 CTTATCACATTATATTACAATTTCACATTCATCACATCGGCCATTAGGCC
1 CTTATCACA-TATA-TACACTTTCACATTCATCACATCGGCCATTAGG-C
2922 CTATATCACATATAT-CACTTTCACATTTTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACA--TTCATCACATCGGCCATTAGGC
2971 CTTA-CACATCATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACAT-ATATACACTTTCACATTCATCACATCGGCCATTAGGC
3018 CTTATCACATATATACACTTTCA-ATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3064 CTTATCACATATATTTACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATA--TACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
3113 GTTATCACATATATACAC--T----TTGATGA-ATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3153 CTTATCACATATATAACACTTTCACA-TCATCACATCGG-C-TTAGGC
1 CTTATCACATATAT-ACACTTTCACATTCATCACATCGGCCATTAGGC
*
3198 CTTATCACATATTTACAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3244 CTTTATCACATATATACACTTTTCACATTCATCACATCGGCCATTAGGC
1 C-TTATCACATATATACAC-TTTCACATTCATCACATCGGCCATTAGGC
3293 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3340 CTTATCACAATATATATACACTTTCACATTCATTCACATCGGCCATTAGGC
1 CTTATCAC---ATATATACACTTTCACATTCA-TCACATCGGCCATTAGGC
* *
3391 TTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * ** *
3438 CTTATACACAGGCCT-TAT-CACATAT-ATATACACTTCACATTCATTCACA-TCGGC
1 CTTAT-CACA----TATATACAC-TTTCACATTCA--TCACA-TC-GGC-CATTAGGC
*
3492 CATTAGGC-CTATCACTTAATTACACTTTTCAC-TTCATCACATCGGCCATTAGGC
1 C-TTA-TCAC-AT-A--T-A-TACAC-TTTCACATTCATCACATCGGCCATTAGGC
3546 CTTATCAACATATATACACTTTCACATTCATTCACATCGCGCCATTAGGC
1 CTTATC-ACATATATACACTTTCACATTCA-TCACATCG-GCCATTAGGC
3596 CTTATCACATATATACACTTTCACATTCATCAACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATC-ACATCGGCCATTAGGC
****
3644 CTTATCACATATATACACTTTCACATTCATTCACATCGGCCACCTCCCCCCC
1 CTTATCACATATATACACTTTCACATTCA-TCACATCGGCCA--T--TAGGC
* * * * ** *
3696 CATTAGCGGC-T-TATTCACATATAT-ACACTT-TTCACATTCATCAATCGGCCATTAGGC
1 C-TTATC-ACATATATACAC-T-T-TCACA-TTCATCACA-TCGGCCAT-------TAGGC
**
3753 GC-TATCACACATATATACACTTTCACATTCATCACATCGGCCATAGCCTTATCCAC
1 -CTTAT--CACATATATACACTTTCACATTCATCACATCGGCC--A---TTA--GGC
* *
3809 ACATATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
1 -CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3857 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3904 CTTATCAAATAT-TACACTTTCACATTCATCACAT-GGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3949 CTTATCACATATATACACTTTCACATTCATCACATCGGCGGCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGC--CATTAGGC
3998 CTTATCACATATATACACTTTCA-ATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4044 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4091 CTTATCACATATAATATTATACACGCTTCACATTCATCACATCGGCCATTAGG-
1 CTTATCAC-----ATA-TATACAC-TTTCACATTCATCACATCGGCCATTAGGC
*
4144 CTTATCACATATATACACTTTCGCATTCATCACATCGGCCATTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
4188 CGCCATACTA
Statistics
Matches: 1471, Mismatches: 94, Indels: 253
0.81 0.05 0.14
Matches are distributed among these distances:
40 27 0.02
41 9 0.01
43 9 0.01
44 62 0.04
45 108 0.07
46 188 0.13
47 249 0.17
48 211 0.14
49 239 0.16
50 114 0.08
51 49 0.03
52 20 0.01
53 36 0.02
54 51 0.03
55 47 0.03
56 16 0.01
57 15 0.01
58 13 0.01
59 7 0.00
61 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:3463 original size:60 final size:61
Alignment explanation
Indices: 3387--3501 Score: 180
Period size: 62 Copynumber: 1.9 Consensus size: 61
3377 ATCGGCCATT
* *
3387 AGGCTTTATCAC-ATATATACACTTTCATATTCA-TCACATCGGCCATTAGGCCTTATACAC
1 AGGCCTTATCACAATATATACAC-TTCACATTCATTCACATCGGCCATTAGGCCTTATACAC
3447 AGGCCTTATCACATATATATACACTTCACATTCATTCACATCGGCCATTAGGCCT
1 AGGCCTTATCACA-ATATATACACTTCACATTCATTCACATCGGCCATTAGGCCT
3502 ATCACTTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
60 11 0.22
61 9 0.18
62 30 0.60
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (61 bp):
AGGCCTTATCACAATATATACACTTCACATTCATTCACATCGGCCATTAGGCCTTATACAC
Found at i:3530 original size:253 final size:244
Alignment explanation
Indices: 2503--4188 Score: 1957
Period size: 241 Copynumber: 6.9 Consensus size: 244
2493 CGGCCCTTAC
* *
2503 ATATATACACTAT-ACATTCATTACATTGGCCATTAGGCCTTATCACATAT-TACACTTTCACAT
1 ATATATACACT-TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
** * * *
2566 TCATCACAT-GGCTCCGTA-GTCTTATCAC--ATATACACGTTCACATTCATCACATCGCCCATT
65 TCATCACATCGGC-CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATT
2627 AGGCCTTATTCACATATGATAACACTTTCACATTCATTCACATCGG-CATTAGGCCTTATACACA
129 AGGCCTTA-TCACATAT-AT-ACACTTTCACATTCA-TCACATCGGCCATTAGGCCTTAT-CACA
2691 TTATATACACTTTCACATTCATCACATC-GCC---A--T-T--AGGCCTTATCACAT
189 -TATATACACTTTCACATTCATCACATCGGCCATTACCTATACAGGCCTTATCACAT
* *
2739 ATATATACACTTTCGCATTCATCACATCGGCCATTAGGCCCTATACACATATAATACACTTTCAC
1 ATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTAT-CACATAT-ATACACTTTCAC
**
2804 ATTCATCACATCGGCCATTATTCCTTA-CACATATATACACTTTCA-ATTCATCACATCGGCCAT
63 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCAT
*
2867 TAGGCCTTATCACATTATATTACAATTTCACATTCATCACATCGGCCATTAGGCCCTATATCACA
128 TAGGCCTTATCACA-TATA-TACACTTTCACATTCATCACATCGGCCATTAGG-CCT-TATCACA
2932 TATAT-CACTTTCACATTTTCATCACATCGGCC---A--T-T--AGGCCTTA-CACAT
189 TATATACACTTTCACA--TTCATCACATCGGCCATTACCTATACAGGCCTTATCACAT
*
2980 -CATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCA-AT
1 ATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
3043 TCATCACATCGGCCATTAGGCCTTATCACATATATTTACACTTTCACATTCATCACATCGGCCAT
65 TCATCACATCGGCCATTAGGCCTTATCACATATA--TACACTTTCACATTCATCACATCGGCCAT
* * *
3108 TAGGCGTTATCACATATATACAC--T----TTGATGA-ATCGGCCATTAGGCCTTATCACATATA
128 TAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
3166 TAACACTTTCACA-TCATCACATCGG-------CT-T--AGGCCTTATCACAT
193 T-ACACTTTCACATTCATCACATCGGCCATTACCTATACAGGCCTTATCACAT
3208 AT-T-TACACTTCACATTCATCACATCGGCCATTAGGCCTTTATCACATATATACACTTTTCACA
1 ATATATACACTTCACATTCATCACATCGGCCATTAGGCC-TTATCACATATATACAC-TTTCACA
3271 TTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATT
64 TTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATT
*
3336 AGGCCTTATCACAATATATATACACTTTCACATTCATTCACATCGGCCATTAGGCTTTATCACAT
129 AGGCCTTATCAC---ATATATACACTTTCACATTCA-TCACATCGGCCATTAGGCCTTATCACAT
*
3401 ATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATACACAGGCCTTATCACAT
190 ATATACACTTTCACATTCATCACATCGGCCATTA--CC-TAT--ACAGGCCTTATCACAT
*
3461 ATATATACACTTCACATTCATTCACATCGGCCATTAGGCC-TATCACTTA-ATTACACTTTTCAC
1 ATATATACACTTCACATTCA-TCACATCGGCCATTAGGCCTTATCACATATA-TACAC-TTTCAC
3524 -TTCATCACATCGGCCATTAGGCCTTATCAACATATATACACTTTCACATTCATTCACATCGCGC
63 ATTCATCACATCGGCCATTAGGCCTTATC-ACATATATACACTTTCACATTCA-TCACATCG-GC
3588 CATTAGGCCTTATCACATATATACACTTTCACATTCATCAACATCGGCCATTAGGCCTTATCACA
125 CATTAGGCCTTATCACATATATACACTTTCACATTCATC-ACATCGGCCATTAGGCCTTATCACA
** *
3653 TATATACACTTTCACATTCATTCACATCGGCCACCTCCCCCCCCATTAGC-GG-CTTATTCACAT
189 TATATACACTTTCACATTCA-TCACATCGGCCA--T---TACCTA-TA-CAGGCCTTA-TCACAT
* **
3716 ATATACACTTTTCACATTCATCA-ATCGGCCATTAGGCGC-TATCACACATATATACACTTTCAC
1 ATATATACACTTCACATTCATCACATCGGCCATTAGGC-CTTAT--CACATATATACACTTTCAC
** * *
3779 ATTCATCACATCGGCCATAGCCTTATCCACACATATCACATATATACACTTTCACATCCATCACA
63 ATTCATCACATCGGCC--A---TTA--GGC-CTTATCACATATATACACTTTCACATTCATCACA
3844 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
120 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
*
3909 CAAATAT-TACACTTTCACATTCATCACAT-GGCC---A--T-T--AGGCCTTATCAC--
185 CACATATATACACTTTCACATTCATCACATCGGCCATTACCTATACAGGCCTTATCACAT
3957 ATATATACACTTTCACATTCATCACATCGGCGGCATTAGGCCTTATCACATATATACACTTTCA-
1 ATATATACAC-TTCACATTCATCACATCGGC--CATTAGGCCTTATCACATATATACACTTTCAC
*
4021 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCATATTCATCACATCGGCCAT
63 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCAT
*
4086 TAGGCCTTATCACATATAATATTATACACGCTTCACATTCATCACATCGGCCATTAGG-CTTATC
128 TAGGCCTTATCAC-----ATA-TATACAC-TTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
4150 ACATATATACACTTTCGCATTCATCACATCGGCCATTAC
186 ACATATATACACTTTCACATTCATCACATCGGCCATTAC
4189 GCCATACTAT
Statistics
Matches: 1290, Mismatches: 54, Indels: 202
0.83 0.03 0.13
Matches are distributed among these distances:
226 29 0.02
227 73 0.06
228 11 0.01
229 48 0.04
230 22 0.02
231 3 0.00
232 24 0.02
233 5 0.00
234 52 0.04
235 1 0.00
236 14 0.01
237 68 0.05
238 65 0.05
239 33 0.03
240 133 0.10
241 146 0.11
242 62 0.05
243 30 0.02
244 5 0.00
245 13 0.01
247 1 0.00
248 1 0.00
249 1 0.00
252 2 0.00
253 123 0.10
254 67 0.05
255 55 0.04
256 65 0.05
257 8 0.01
258 7 0.01
259 16 0.01
260 27 0.02
261 44 0.03
262 8 0.01
263 23 0.02
264 5 0.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (244 bp):
ATATATACACTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
CATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAG
GCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTACCTATACAGGCCTTATCACAT
Found at i:3536 original size:108 final size:111
Alignment explanation
Indices: 3336--3550 Score: 350
Period size: 108 Copynumber: 2.0 Consensus size: 111
3326 ATCGGCCATT
*
3336 AGGCCTTATCACAATATATATACACTTTCACATTCATTCACATCGGCCATTAGGCTTTATCACAT
1 AGGCCTTATCACAATATATATACACTTTCACATTCATTCACATCGGCCATTAGGCTCTATCACAT
3401 ATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATACAC
66 ATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATACAC
*
3447 AGGCCTTATCAC-ATATATATACAC-TTCACATTCATTCACATCGGCCATTAGGC-CTATCACTT
1 AGGCCTTATCACAATATATATACACTTTCACATTCATTCACATCGGCCATTAGGCTCTATCACAT
*
3509 A-ATTACACTTTTCA-CTTCATCACATCGGCCATTAGGCCTTAT
66 ATA-TACAC-TTTCATATTCATCACATCGGCCATTAGGCCTTAT
3551 CAACATATAT
Statistics
Matches: 99, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
107 1 0.01
108 40 0.40
109 34 0.34
110 12 0.12
111 12 0.12
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.33
Consensus pattern (111 bp):
AGGCCTTATCACAATATATATACACTTTCACATTCATTCACATCGGCCATTAGGCTCTATCACAT
ATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATACAC
Found at i:10065 original size:14 final size:13
Alignment explanation
Indices: 10042--10073 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
10032 GGGATATCAA
10042 AACAATAATTAAG
1 AACAATAATTAAG
10055 AACACATAATTAAG
1 AACA-ATAATTAAG
10069 AACAA
1 AACAA
10074 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:14477 original size:40 final size:40
Alignment explanation
Indices: 14423--14584 Score: 243
Period size: 40 Copynumber: 4.0 Consensus size: 40
14413 TGAGAGTTAT
*
14423 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
14463 TTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * *
14503 ATATATCCGGGCTAAGTCTCGAAGATCATTCGTGCTACTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * * *
14543 ATATATCCAGGCTAAGTCCCGAAGAGCAATCATGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
14583 AT
1 AT
14585 GTGTATTCGG
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 109 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
Found at i:14795 original size:25 final size:25
Alignment explanation
Indices: 14745--14795 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
14735 TGTGTAACAA
* *
14745 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
14770 CAAATGATTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
14795 C
1 C
14796 GAGTTATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:16204 original size:31 final size:31
Alignment explanation
Indices: 16161--16224 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
16151 CCTTTTCATA
*
16161 TTTCATAATTCATAACACTGGGTCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* ** *
16192 TTTCATATTTCATATTATTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
16223 TT
1 TT
16225 ACTGTAAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:16517 original size:47 final size:47
Alignment explanation
Indices: 16442--16534 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
16432 GCCTCTTTTA
16442 ATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCACTTTG
1 ATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCACTTTG
* * * *
16489 ATAATTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCACTTT
16535 TGCACTTCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (47 bp):
ATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCACTTTG
Found at i:16536 original size:24 final size:24
Alignment explanation
Indices: 16431--16536 Score: 151
Period size: 24 Copynumber: 4.4 Consensus size: 24
16421 CTGGAGGCCT
* *
16431 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTGATAACTGGGGCATA
*
16456 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
* *
16480 AGCAC-TTTGATAATTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
16503 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
16527 AGCCCTTTTG
1 AGCCCTTTTG
16537 CACTTCCTCC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.27
24 50 0.68
25 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTGATAACTGGGGCATA
Found at i:16607 original size:9 final size:9
Alignment explanation
Indices: 16593--16649 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
16583 ATCTCATGTG
16593 CATATCATA
1 CATATCATA
*
16602 CATATCATGTG
1 CATATCA--TA
16613 CATATCATA
1 CATATCATA
* *
16622 CATGTCATGTG
1 CATATCA--TA
16633 CATATCATA
1 CATATCATA
16642 CATATCAT
1 CATATCAT
16650 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:16609 original size:20 final size:20
Alignment explanation
Indices: 16581--16651 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
16571 GCATTTATGA
*
16581 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
16601 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
16621 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
16641 ACATATCATGT
1 ACATATCATGT
16652 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:16616 original size:11 final size:11
Alignment explanation
Indices: 16586--16640 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
16576 TATGAACATC
16586 TCATGTGCATA
1 TCATGTGCATA
*
16597 TCA--TACATA
1 TCATGTGCATA
16606 TCATGTGCATA
1 TCATGTGCATA
* *
16617 TCA--TACATG
1 TCATGTGCATA
16626 TCATGTGCATA
1 TCATGTGCATA
16637 TCAT
1 TCAT
16641 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:16729 original size:25 final size:24
Alignment explanation
Indices: 16687--16734 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
16677 CATATATAAC
* * *
16687 CCTAGGGGTATAATGGTCACTTTTA
1 CCTAGGGGCAAAACGGTCA-TTTTA
16712 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
16735 CATGTTATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (24 bp):
CCTAGGGGCAAAACGGTCATTTTA
Found at i:30191 original size:14 final size:15
Alignment explanation
Indices: 30174--30202 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30164 TCACAAAAAC
30174 TTCACACAT-ATAAA
1 TTCACACATAATAAA
30188 TTCACACATAATAAA
1 TTCACACATAATAAA
30203 CACTGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:31606 original size:32 final size:32
Alignment explanation
Indices: 31565--31642 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
31555 CATAAAGGGA
*
31565 CACACGCCCATGTAGATTGGGCTGTGTGGACT
1 CACACGCCCATGTAGATTGGGCCGTGTGGACT
31597 CACACGCCCATGTAGATTGGGCCGTGTGGACT
1 CACACGCCCATGTAGATTGGGCCGTGTGGACT
*
31629 CACACGCCCGTGTA
1 CACACGCCCATGTA
31643 ACTTGAGGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.22
Consensus pattern (32 bp):
CACACGCCCATGTAGATTGGGCCGTGTGGACT
Done.