Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1173
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: 58854
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:733 original size:11 final size:12
Alignment explanation
Indices: 711--762 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 12
701 AGGAAGCGGA
*
711 GTATGCCCGGAG
1 GTATGCCTGGAG
723 GTA-GCCTGGAG
1 GTATGCCTGGAG
734 G-ATGCCTGGA-
1 GTATGCCTGGAG
*
744 GCATGCCT-GAG
1 GTATGCCTGGAG
755 GTA-GCCTG
1 GTATGCCTG
763 AGCATGCCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 8 0.24
11 23 0.68
12 3 0.09
ACGTcount: A:0.17, C:0.23, G:0.40, T:0.19
Consensus pattern (12 bp):
GTATGCCTGGAG
Found at i:22135 original size:37 final size:37
Alignment explanation
Indices: 22085--22163 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
22075 TTATTACGAA
* * *
22085 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
22122 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
22159 GTCTT
1 GTCTT
22164 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:22360 original size:47 final size:45
Alignment explanation
Indices: 22286--22587 Score: 310
Period size: 47 Copynumber: 6.9 Consensus size: 45
22276 TCGGGACTTA
* * * * *
22286 TCACATTTATACACTTTCACATCCATCACGTTGGCCACTCAGCCCT
1 TCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGCCCT
*
22332 GTCACATATATACACTTCCACATTCATCACATCGGCC---A----T
1 -TCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCCT
*
22371 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCCT
* *
22417 ATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 -TCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCCT
* *
22464 ATCAATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 -TC-ACATATATACACTTTCACATTCATCACATCGGCCATTAGCCCT
*
22511 T-ATATATATACAC-TTCACATTCATCACATCGGCCATTA-----
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCCT
*
22549 -CATATATATACACTTTCACATTCATCACATCGGCACATT
1 TCACATATATACACTTTCACATTCATCACATCGGC-CATT
22588 CATCACATCG
Statistics
Matches: 231, Mismatches: 11, Indels: 33
0.84 0.04 0.12
Matches are distributed among these distances:
38 47 0.20
39 21 0.09
40 4 0.02
41 1 0.00
43 26 0.11
44 12 0.05
46 2 0.01
47 82 0.35
48 36 0.16
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (45 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCCT
Found at i:22384 original size:38 final size:39
Alignment explanation
Indices: 22334--22587 Score: 251
Period size: 38 Copynumber: 6.0 Consensus size: 39
22324 TCAGCCCTGT
*
22334 CACATATATACACTTCCACATTCATCACATCGGCCATT-
1 CACATATATACACTTTCACATTCATCACATCGGCCATTG
22372 CACATATATACACTTTCACATTCATCACATCGGCCATTAGG
1 CACATATATACACTTTCACATTCATCACATCGGCCATT--G
22413 CCTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGG
1 -C--A-CA--TATATACACTTTCACATTCATCACATCGGCCATT--G
22460 CCTTATCAATATATATACACTTTCACATTCATCACATCGGCCATTAGG
1 -C--A-C---ATATATACACTTTCACATTCATCACATCGGCCATT--G
* *
22508 CCTTATATATATACAC-TTCACATTCATCACATCGGCCATTA
1 -C--ACATATATACACTTTCACATTCATCACATCGGCCATTG
*
22549 CATATATATACACTTTCACATTCATCACATCGGCACATT
1 CACATATATACACTTTCACATTCATCACATCGGC-CATT
22588 CATCACATCG
Statistics
Matches: 199, Mismatches: 3, Indels: 26
0.87 0.01 0.11
Matches are distributed among these distances:
38 49 0.25
39 20 0.10
40 5 0.03
42 1 0.01
43 24 0.12
44 11 0.06
45 2 0.01
47 44 0.22
48 42 0.21
50 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.32
Consensus pattern (39 bp):
CACATATATACACTTTCACATTCATCACATCGGCCATTG
Found at i:22398 original size:85 final size:83
Alignment explanation
Indices: 22287--22587 Score: 354
Period size: 85 Copynumber: 3.5 Consensus size: 83
22277 CGGGACTTAT
* * * * *
22287 CACATTTATACACTTTCACATCCATCACGTTGGCCACTCAGCCCTGTCACATATATACACTTCCA
1 CACATATATACACTTTCACATTCATCACATCGGCCA-TTAGCCCT-TCACATATATACACTT-CA
22352 CATTCATCACATCGGCCATT-
63 CATTCATCACATCGGCCATTA
* *
22372 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCCT-TCACATATATACAC-TTCA
22437 CATTCATCACATCGGCCATTA
63 CATTCATCACATCGGCCATTA
* *
22458 GGCCTTATCAATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT-ATATATATAC
1 ---C--A-C---ATATATACACTTTCACATTCATCACATCGGCCATTAGCCCTTCACATATATAC
22522 ACTTCACATTCATCACATCGGCCATTA
57 ACTTCACATTCATCACATCGGCCATTA
*
22549 CATATATATACACTTTCACATTCATCACATCGGCACATT
1 CACATATATACACTTTCACATTCATCACATCGGC-CATT
22588 CATCACATCG
Statistics
Matches: 190, Mismatches: 13, Indels: 28
0.82 0.06 0.12
Matches are distributed among these distances:
82 31 0.16
83 4 0.02
84 2 0.01
85 71 0.37
86 3 0.02
88 1 0.01
89 1 0.01
91 26 0.14
92 11 0.06
93 1 0.01
94 3 0.02
95 36 0.19
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.32
Consensus pattern (83 bp):
CACATATATACACTTTCACATTCATCACATCGGCCATTAGCCCTTCACATATATACACTTCACAT
TCATCACATCGGCCATTA
Found at i:22587 original size:17 final size:17
Alignment explanation
Indices: 22565--22603 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
22555 TATACACTTT
22565 CACATTCATCACATCGG
1 CACATTCATCACATCGG
22582 CACATTCATCACATCGG
1 CACATTCATCACATCGG
22599 C-CATT
1 CACATT
22604 AGCCCTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.28, C:0.36, G:0.10, T:0.26
Consensus pattern (17 bp):
CACATTCATCACATCGG
Found at i:22615 original size:47 final size:47
Alignment explanation
Indices: 22582--22892 Score: 527
Period size: 47 Copynumber: 6.6 Consensus size: 47
22572 ATCACATCGG
22582 CACATTCATCACATCGGCCATTA-GCCCTATCACATATATACAC-TT
1 CACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTT
* *
22627 CACATTCATCACATCGGCCATTAGGCCTTATCTCATATATACACTTT
1 CACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTT
*
22674 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTT
1 CACATTCATCACATCGGCCATTAGGCCCTATCACATATAT--ACACTTT
22723 CACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACACTTT
1 CACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATATACACTTT
*
22772 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
1 CACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTT
*
22819 CACATTCATCACATCGGCCATTAGGCCCTATCACGTATATACACTTT
1 CACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTT
22866 CACATTCATCACATCGGCCATTAGGCC
1 CACATTCATCACATCGGCCATTAGGCC
22893 TTACTATCAT
Statistics
Matches: 253, Mismatches: 7, Indels: 10
0.94 0.03 0.04
Matches are distributed among these distances:
45 23 0.09
46 18 0.07
47 126 0.50
49 80 0.32
51 6 0.02
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.30
Consensus pattern (47 bp):
CACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTT
Found at i:22705 original size:239 final size:237
Alignment explanation
Indices: 22371--22895 Score: 794
Period size: 239 Copynumber: 2.2 Consensus size: 237
22361 CATCGGCCAT
*
22371 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
*
22436 ACATTCATCACATCGGCCATTAGGCCTTATCA-ATATATATACACTTTCACATTCATCACATCGG
66 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGG
*
22500 CCATTAGG-CCT-T-ATATATATACAC-TTCACATTCATCACATCGGCCATTACATATATATACA
131 CCATTAGGCCCTATCATATATATACACTTTCACATTCATCACATCGGCCATTACACAT-TAT-CA
*
22561 CTTTCACATTCATCACATCGGCACATTCATCACATCGGCCATTA-GCCCTA
194 C-AT-ACA-T-A-CAC-T-GGCACATTCATCACATCGGCCATTAGGCCCTA
*
22611 TCACATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
22675 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGG
66 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGG
** *
22740 CCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
131 CCATTAGGCCCTAT--CATATATATACACTTTCACATTCATCACATCGGCCATTACACATTATCA
* **
22805 CATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTA
194 CATACATACACTGGCACATTCATCACATCGGCCATTAGGCCCTA
*
22849 TCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
22896 CTATCATTTC
Statistics
Matches: 264, Mismatches: 12, Indels: 19
0.89 0.04 0.06
Matches are distributed among these distances:
237 23 0.09
238 20 0.08
239 115 0.44
240 54 0.20
241 4 0.02
242 3 0.01
243 1 0.00
244 3 0.01
245 15 0.06
246 26 0.10
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (237 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGG
CCATTAGGCCCTATCATATATATACACTTTCACATTCATCACATCGGCCATTACACATTATCACA
TACATACACTGGCACATTCATCACATCGGCCATTAGGCCCTA
Found at i:22837 original size:192 final size:187
Alignment explanation
Indices: 22375--22895 Score: 748
Period size: 192 Copynumber: 2.7 Consensus size: 187
22365 GGCCATTCAC
*
22375 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
22440 TCATCACATCGGCCATTAGGCCTTATCAAT-ATATATACACTTTCACATTCATCACATCGGCCAT
66 TCATCACATCGGCCATTAGGCCTTATC--TCATATATACACTTTCACATTCATCACATCGGCCAT
* *
22504 TAGGCCTTATATATATACACTTCACATTCATCACATCGGCCATTACATATATATACACT
129 TAGGCCTTATATATATACACTTCACATTCATCACATCGGCCATTACACATATACACACT
* * ** *
22563 TTCACATTCATCACATCGGCACATTCATCACATCGGCCATTA-GCCCTATCACATATATACAC-T
1 AT-ATA-T-A-CAC-T-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
22626 TCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATACACTTTCACATTCATCACATCGG
60 TCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATACACTTTCACATTCATCACATCGG
*
22691 CCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC-CCTAT-
125 CCATTAGGCCTTAT---ATATAT--ACAC-TTCACATTCATCACATCGGCCATTA--CACATATA
22754 CACA-T
182 CACACT
22759 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
* * *
22824 TCATCACATCGGCCATTAGGCCCTATCACGTATATACACTTTCACATTCATCACATCGGCCATTA
66 TCATCACATCGGCCATTAGGCCTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTA
22889 GGCCTTA
131 GGCCTTA
22896 CTATCATTTC
Statistics
Matches: 299, Mismatches: 17, Indels: 30
0.86 0.05 0.09
Matches are distributed among these distances:
188 1 0.00
189 2 0.01
190 25 0.08
191 65 0.22
192 116 0.39
193 20 0.07
194 30 0.10
195 2 0.01
196 6 0.02
197 28 0.09
198 3 0.01
199 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (187 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTA
GGCCTTATATATATACACTTCACATTCATCACATCGGCCATTACACATATACACACT
Found at i:27302 original size:25 final size:25
Alignment explanation
Indices: 27270--27322 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
27260 CTTATCTAAC
27270 AACCAAGCTTAATAATCTTTCATCA
1 AACCAAGCTTAATAATCTTTCATCA
27295 AACCAAGCTTAATAATCTTTCATCA
1 AACCAAGCTTAATAATCTTTCATCA
27320 AAC
1 AAC
27323 TTCAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.30
Consensus pattern (25 bp):
AACCAAGCTTAATAATCTTTCATCA
Found at i:36534 original size:12 final size:12
Alignment explanation
Indices: 36517--36541 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36507 GTTTCCACTT
36517 TGCTGGAATTTC
1 TGCTGGAATTTC
36529 TGCTGGAATTTC
1 TGCTGGAATTTC
36541 T
1 T
36542 AGTGTGACAA
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:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (12 bp):
TGCTGGAATTTC
Found at i:40689 original size:11 final size:11
Alignment explanation
Indices: 40673--40697 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40663 ATATGATATT
40673 TTATTATTTTA
1 TTATTATTTTA
40684 TTATTATTTTA
1 TTATTATTTTA
40695 TTA
1 TTA
40698 ATATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:42836 original size:4 final size:4
Alignment explanation
Indices: 42814--42850 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
42804 CAAATTAAAA
*
42814 AATT AA-T AACT AA-T AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AAT
42851 CTAAAATATC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (4 bp):
AATT
Found at i:46207 original size:56 final size:56
Alignment explanation
Indices: 46116--46238 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
46106 GAGATTGGCG
* * *
46116 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
46173 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
46228 CTGAGTGTGCG
1 CTAAGTGTGCG
46239 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:46225 original size:27 final size:28
Alignment explanation
Indices: 46116--46238 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
46106 GAGATTGGCG
* * * *
46116 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
46145 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
46173 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
46201 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
46228 CTGAGTGTGCG
1 CTAAGTGTGCG
46239 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:46249 original size:27 final size:27
Alignment explanation
Indices: 46141--46251 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
46131 TAAATTGTAC
* * *
46141 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
46169 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
46197 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
46224 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
46251 A
1 A
46252 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:54353 original size:29 final size:30
Alignment explanation
Indices: 54318--54407 Score: 134
Period size: 29 Copynumber: 3.1 Consensus size: 30
54308 ACATCATTAA
*
54318 TGTGTGCGAGTTTGATTATGTAG-ACTAAG
1 TGTGTGCGAGTTTGATTATATAGCACTAAG
54347 TGTGTGCGAGTTTGATTATATAGCACTAA-
1 TGTGTGCGAGTTTGATTATATAGCACTAAG
*
54376 -GTGTGCGAG-TTGATTATATAGCACTGAG
1 TGTGTGCGAGTTTGATTATATAGCACTAAG
54404 TGTG
1 TGTG
54408 CGGACTTAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
27 17 0.30
28 9 0.16
29 25 0.45
30 5 0.09
ACGTcount: A:0.24, C:0.09, G:0.30, T:0.37
Consensus pattern (30 bp):
TGTGTGCGAGTTTGATTATATAGCACTAAG
Found at i:54395 original size:27 final size:28
Alignment explanation
Indices: 54319--54409 Score: 132
Period size: 27 Copynumber: 3.2 Consensus size: 28
54309 CATCATTAAT
*
54319 GTGTGCGAGTTTGATTATGTAG-ACTAA
1 GTGTGCGAGTTTGATTATATAGCACTAA
54346 GTGTGTGCGAGTTTGATTATATAGCACTAA
1 --GTGTGCGAGTTTGATTATATAGCACTAA
*
54376 GTGTGCGAG-TTGATTATATAGCACTGA
1 GTGTGCGAGTTTGATTATATAGCACTAA
54403 GTGTGCG
1 GTGTGCG
54410 GACTTAATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
27 24 0.41
28 9 0.15
29 21 0.36
30 5 0.08
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (28 bp):
GTGTGCGAGTTTGATTATATAGCACTAA
Found at i:54420 original size:27 final size:27
Alignment explanation
Indices: 54348--54422 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
54338 TAGACTAAGT
* *
54348 GTGTGCGAGTTTGATTATATAGCACTAA
1 GTGTGCGA-CTTGAATATATAGCACTAA
* * *
54376 GTGTGCGAGTTGATTATATAGCACTGA
1 GTGTGCGACTTGAATATATAGCACTAA
54403 GTGTGCGGACTT-AATATATA
1 GTGTGC-GACTTGAATATATA
54423 CTTTTTGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 30 0.71
28 12 0.29
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.35
Consensus pattern (27 bp):
GTGTGCGACTTGAATATATAGCACTAA
Done.