Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold399
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: 45606
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Found at i:433 original size:40 final size:40
Alignment explanation
Indices: 388--574 Score: 233
Period size: 40 Copynumber: 4.7 Consensus size: 40
378 ACTACTTGCT
* *
388 CAAATG-CTTCGTTGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCG-GGACTTAGCCCGGTTATAGTAACTAGCA
*
428 CAAATGCCTTCGGGACTTAGAGCCCGGATAATAGT-ACTAGCA
1 CAAATGCCTTCGGGACTT--AGCCCGG-TTATAGTAACTAGCA
* *
470 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
* *
510 CAAATGCCTTCGGGACTTAG-CC-G--AAAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
546 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
575 CATCCGAATA
Statistics
Matches: 128, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
36 30 0.23
37 2 0.02
38 2 0.02
39 7 0.05
40 45 0.35
41 5 0.04
42 31 0.24
43 6 0.05
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
Found at i:494 original size:82 final size:76
Alignment explanation
Indices: 388--574 Score: 270
Period size: 82 Copynumber: 2.4 Consensus size: 76
378 ACTACTTGCT
*
388 CAAATG-CTTCGTTGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGAGCC
1 CAAATGCCTTCG-GGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT--AG-C
452 CGGATAATAGT-ACTAGCA
62 C-G--AA-AGTCACTAGCA
*
470 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGAA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGAA
535 AGTCACTAGCA
66 AGTCACTAGCA
546 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
575 CATCCGAATA
Statistics
Matches: 100, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
75 3 0.03
76 37 0.37
78 1 0.01
79 2 0.02
80 2 0.02
82 50 0.50
83 5 0.05
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (76 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGAA
AGTCACTAGCA
Found at i:8498 original size:40 final size:40
Alignment explanation
Indices: 8314--8498 Score: 302
Period size: 40 Copynumber: 4.6 Consensus size: 40
8304 ACTACTTGCT
8314 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TATAGTAACTCGCA
*
8354 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
8394 CAAATGCCTTCGGGACTTAGACCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
8434 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
8474 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
8499 TTATCATCCG
Statistics
Matches: 137, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
39 1 0.01
40 134 0.98
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:10233 original size:48 final size:48
Alignment explanation
Indices: 10162--10406 Score: 427
Period size: 48 Copynumber: 5.1 Consensus size: 48
10152 GGCTGTCACA
* *
10162 ACCACAAATACATATCTCATACATATTTCACATTAGCCATTCGGCTTT
1 ACCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTT
* *
10210 ACCACATATACATATCTCATACATACTTCACATTAGCCATTCGGCTTT
1 ACCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTT
* *
10258 ACCACATATACATATCTCATATATATTTCACACTAGCCATTCGACTTT
1 ACCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTT
*
10306 ACCACATATACATATCTCATATATATTTCACACTAGCCATTCGGCTTT
1 ACCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTT
10354 ACCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTT
1 ACCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTT
10402 ACCAC
1 ACCAC
10407 GCACATATAT
Statistics
Matches: 189, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 189 1.00
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (48 bp):
ACCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTT
Found at i:21255 original size:20 final size:20
Alignment explanation
Indices: 21150--21257 Score: 74
Period size: 20 Copynumber: 5.4 Consensus size: 20
21140 GATTGCATTT
*
21150 TGGTGCCTCTATTTGCACT-
1 TGGTGCCTCTGTTTGCACTA
* * ** *
21169 TCAGTGCCTCTGCTTATACTT
1 T-GGTGCCTCTGTTTGCACTA
* *
21190 TGGTGTCGCTGTTTGCACTA
1 TGGTGCCTCTGTTTGCACTA
* * * *
21210 TGATGACTCTGATTGCACAA
1 TGGTGCCTCTGTTTGCACTA
*
21230 TTGTGCCTCTGTTTGCACTA
1 TGGTGCCTCTGTTTGCACTA
*
21250 CGGTGCCT
1 TGGTGCCT
21258 TTGTATAGCA
Statistics
Matches: 63, Mismatches: 24, Indels: 3
0.70 0.27 0.03
Matches are distributed among these distances:
19 1 0.02
20 61 0.97
21 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.39
Consensus pattern (20 bp):
TGGTGCCTCTGTTTGCACTA
Found at i:23397 original size:29 final size:26
Alignment explanation
Indices: 23327--23397 Score: 61
Period size: 29 Copynumber: 2.5 Consensus size: 26
23317 TAAAAGTCCT
* *
23327 TTTTTTTTTGGTCATCCAACTATGAA
1 TTTTTTTTTGGTCACCCAACTATAAA
*
23353 TTTTTTTAAATAGGTCACCCAACTAATTAAGA
1 TTTTTTT---TTGGTCACCCAACT-A-TAA-A
23385 TTTTTTTTTGGTC
1 TTTTTTTTTGGTC
23398 CACTTCCGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
26 7 0.20
29 17 0.49
30 1 0.03
31 2 0.06
32 8 0.23
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (26 bp):
TTTTTTTTTGGTCACCCAACTATAAA
Found at i:26643 original size:47 final size:47
Alignment explanation
Indices: 26572--26976 Score: 657
Period size: 47 Copynumber: 8.6 Consensus size: 47
26562 CCCTTCGGGA
* * * * * * *
26572 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCGACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
26619 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26666 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26713 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26760 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26807 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
26854 CTTATCACATATATATACACTTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26903 CTTATCACATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26950 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
26977 TATTCAAATA
Statistics
Matches: 340, Mismatches: 16, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
47 296 0.87
49 44 0.13
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31029 original size:40 final size:40
Alignment explanation
Indices: 30997--31423 Score: 675
Period size: 40 Copynumber: 10.8 Consensus size: 40
30987 CCAGCATGAT
* * * * *
30997 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* ** * *
31037 TGCTCTTTGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** *
31077 TGCTCTTCGAAACTTAGTCCGGATACATCACT---A-GAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
31113 TGCTCTTTGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
31153 TGCTCTTCGGGGCTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
31193 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
31233 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
31273 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
31313 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
31353 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
31392 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
31424 CTCAATTCTC
Statistics
Matches: 359, Mismatches: 23, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
36 32 0.09
37 1 0.00
39 40 0.11
40 286 0.80
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:32907 original size:25 final size:25
Alignment explanation
Indices: 32879--32957 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
32869 CACTCGGCCT
32879 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
32904 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
32926 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
32951 ATCACAT
1 ATCACAT
32958 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:32947 original size:47 final size:47
Alignment explanation
Indices: 32830--33233 Score: 675
Period size: 47 Copynumber: 8.6 Consensus size: 47
32820 CCGTTCGGGA
* * * * * *
32830 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
32877 C-TATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32923 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
32970 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
33017 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
33064 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
33111 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
33160 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
33207 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
33234 TATTCAAATA
Statistics
Matches: 342, Mismatches: 12, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
46 42 0.12
47 255 0.75
49 45 0.13
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:37440 original size:39 final size:40
Alignment explanation
Indices: 37237--37659 Score: 495
Period size: 39 Copynumber: 10.8 Consensus size: 40
37227 CCAGCATGAT
* * * *
37237 TGCTCTT-GGGACCTAGCCCGGATATAACACCAGCACTGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCAC-GAA
* ** * *
37277 TGCTCTTTGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
37317 TGCTTCTTCGAAACTTAGTCCGGATACATCACT--TA-GAA
1 TGC-TCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
37355 TGCTCTTTGAGACTTAGCCCGGATACATCACTAGCACG-A
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
37394 TGCCTCTTCGGGGCTTAGCCCGGA-AC-TCACTGTAGCA-GAA
1 TG-CTCTTCGGGACTTAGCCCGGATACATCAC--TAGCACGAA
37434 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCAACG-A
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGC-ACGAA
37473 TGCTCTTCGGGAC-TAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
37512 TGCTTCTTCGGGACTTAGCCCGGATACATTCACTAGCAACGAA
1 TGC-TCTTCGGGACTTAGCCCGGATACA-TCACTAGC-ACGAA
37555 TGCTC-TCGGGACTTAG-CCGG-TACATCACT-GCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
37591 TGCTCTTCGGG-CTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
37630 TGCTCTTC-GGAC-TAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
37660 CTCAATTCTC
Statistics
Matches: 336, Mismatches: 23, Indels: 50
0.82 0.06 0.12
Matches are distributed among these distances:
36 15 0.04
37 37 0.11
38 64 0.19
39 71 0.21
40 63 0.19
41 68 0.20
42 10 0.03
43 8 0.02
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:37476 original size:118 final size:117
Alignment explanation
Indices: 37237--37659 Score: 471
Period size: 118 Copynumber: 3.6 Consensus size: 117
37227 CCAGCATGAT
* * * * * * ** *
37237 TGCTCTTGGGACCTAGCCCGGATATAACACCAGCACTGAATG-CTCTTTGGGGTTTAGCACGGAT
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCAC-GAATGCCTCTTCGGGACTTAGCCCGGAT
* *
37301 ATATCACTAGCACGAATGCTTCTTCGAAACTTAGTCCGGATACATCACTTAG-A--A
65 ACATCACTAGCACGAATGC-TCTTCG-GACTTAG-CCGGATACATCAC-TAGCACGA
* *
37355 TGCTCTTTGAGACTTAGCCCGGATACATCACTAGCACG-ATGCCTCTTCGGGGCTTAGCCCGGA-
1 TGCTCTTCG-GACTTAGCCCGGATACATCACTAGCACGAATGCCTCTTCGGGACTTAGCCCGGAT
37418 AC-TCACTGTAGCA-GAATGCTCTTCGGACTTAGCCCGGATACATCACTAGCAACGA
65 ACATCAC--TAGCACGAATGCTCTTCGGACTTAG-CCGGATACATCACTAGC-ACGA
*
37473 TGCTCTTCGGGAC-TAGCCCGGATACATCACTAGCACGAATGCTTCTTCGGGACTTAGCCCGGAT
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAATGCCTCTTCGGGACTTAGCCCGGAT
37537 ACATTCACTAGCAACGAATGCTC-TCGGGACTTAGCCGG-TACATCACT-GCACGAA
65 ACA-TCACTAGC-ACGAATGCTCTTC-GGACTTAGCCGGATACATCACTAGCACG-A
*
37591 TGCTCTTCGGGCTTAGCCCGGATACATCACTAGCACGAATG-CTCTTC-GGAC-TAGCCCGGATA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCCTCTTCGGGACTTAGCCCGGATA
37653 CATCACT
66 CATCACT
37660 CTCAATTCTC
Statistics
Matches: 271, Mismatches: 16, Indels: 40
0.83 0.05 0.12
Matches are distributed among these distances:
114 8 0.03
115 32 0.12
116 15 0.06
117 45 0.17
118 105 0.39
119 39 0.14
120 7 0.03
121 20 0.07
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (117 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCCTCTTCGGGACTTAGCCCGGATA
CATCACTAGCACGAATGCTCTTCGGACTTAGCCGGATACATCACTAGCACGA
Found at i:39211 original size:93 final size:95
Alignment explanation
Indices: 39097--39440 Score: 399
Period size: 91 Copynumber: 3.7 Consensus size: 95
39087 TCGGCCACTC
* * * *
39097 GGCCCTATCA-ATATAAACACTTTCAC-TATCAT-CACATTGGCCATT-CGCCTTATCAACATAA
1 GGCCTTATCACATATACACACTTTCACAT-TCATACACATCGGCCATTAGGCCTTATC-ACATAA
39158 TACACACTTTCACATTCATCACATCGGCATTA
64 TACACACTTTCACATTCATCACATCGGCATTA
* *
39190 GGCCTTATCACATATA-ACACTTTCACA-TCATGCACATCGGCTATTAGGCCTTCATCA-AT-AT
1 GGCCTTATCACATATACACACTTTCACATTCATACACATCGGCCATTAGGCCTT-ATCACATAAT
* *
39251 ATACA-TTCCACA-TC--CACATCGGGCTATTA
65 ACACACTTTCACATTCATCACATC-GGC-ATTA
*
39280 GGCCTTATCACATATATACACTTTCACATTCAT-CACATCGGCCATTAGGCCTTATCACATATAT
1 GGCCTTATCACATATACACACTTTCACATTCATACACATCGGCCATTAGGCCTTATCACATA-AT
* * *
39344 ACATACCTTTCACATTCATCACATTGGCCATTC
65 ACACA-CTTTCACATTCATCACATCGG-CATTA
39377 GGCCTTATCACATATATACACACTTTCACATTCATACACATCGGCCATTAGGCCTTATCACATA
1 GGCCTTATCAC--ATATACACACTTTCACATTCATACACATCGGCCATTAGGCCTTATCACATA
39441 TATAAATTCA
Statistics
Matches: 217, Mismatches: 13, Indels: 35
0.82 0.05 0.13
Matches are distributed among these distances:
88 6 0.03
89 3 0.01
90 26 0.12
91 38 0.18
92 14 0.06
93 37 0.17
94 11 0.05
95 9 0.04
96 2 0.01
97 16 0.07
98 6 0.03
99 21 0.10
100 28 0.13
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.31
Consensus pattern (95 bp):
GGCCTTATCACATATACACACTTTCACATTCATACACATCGGCCATTAGGCCTTATCACATAATA
CACACTTTCACATTCATCACATCGGCATTA
Found at i:39317 original size:91 final size:90
Alignment explanation
Indices: 39055--39453 Score: 377
Period size: 91 Copynumber: 4.3 Consensus size: 90
39045 CCGTTCGGGA
* * * * * *
39055 CTTATCACATTTATACACTTCACATC-CTACGTTCGGCCACTCGGCCCTATCA-ATATAAACACT
1 CTTATCACATATATACA-TTCACATCAC-AC-ATCGG-CATTAGGCCTTATCACATATATACACT
* *
39118 TTCAC-TATCAT-CACATTGGCCATT-CGC
62 TTCACAT-TCATACACATCGGCCATTAGGC
*
39145 CTTATCAACATAATACACACTTTCACATTCATCACATCGGCATTAGGCCTTATCACATATA-ACA
1 CTTATC-ACAT-ATATACA--TTCACA-TCA-CACATCGGCATTAGGCCTTATCACATATATACA
* *
39209 CTTTCACA-TCATGCACATCGGCTATTAGGC
60 CTTTCACATTCATACACATCGGCCATTAGGC
39239 CTTCATCA-ATATATACATTCCACATC-CACATCGGGCTATTAGGCCTTATCACATATATACACT
1 CTT-ATCACATATATACATT-CACATCACACATC-GGC-ATTAGGCCTTATCACATATATACACT
39302 TTCACATTCAT-CACATCGGCCATTAGGC
62 TTCACATTCATACACATCGGCCATTAGGC
* *
39330 CTTATCACATATATACATACCTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
1 CTTATCACATATATAC--A---TTCACA-TCA-CACATCGG-CATTAGGCCTTATCACATATAT-
39395 CACACTTTCACATTCATACACATCGGCCATTAGGC
57 -ACACTTTCACATTCATACACATCGGCCATTAGGC
*
39430 CTTATCACATATATAAATTCACAT
1 CTTATCACATATATACATTCACAT
39454 TTATTCAATA
Statistics
Matches: 265, Mismatches: 15, Indels: 54
0.79 0.04 0.16
Matches are distributed among these distances:
88 6 0.02
89 3 0.01
90 34 0.13
91 46 0.17
92 19 0.07
93 42 0.16
94 18 0.07
95 15 0.06
96 5 0.02
97 22 0.08
98 7 0.03
99 16 0.06
100 32 0.12
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (90 bp):
CTTATCACATATATACATTCACATCACACATCGGCATTAGGCCTTATCACATATATACACTTTCA
CATTCATACACATCGGCCATTAGGC
Found at i:39374 original size:50 final size:48
Alignment explanation
Indices: 39055--39444 Score: 415
Period size: 50 Copynumber: 8.3 Consensus size: 48
39045 CCGTTCGGGA
* * * * *
39055 CTTATCACATTTATAC-AC-TTCACA-TCCT-ACGTTCGGCCACTCGGC
1 CTTATCACATATATACAACTTTCACATTCATCAC-ATCGGCCATTAGGC
* * * *
39100 CCTATCA-ATATAAAC-ACTTTCAC-TATCATCACATTGGCCATT-CGC
1 CTTATCACATATATACAACTTTCACAT-TCATCACATCGGCCATTAGGC
39145 CTTATCAACATA-ATACACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATC-ACATATATACA-ACTTTCACATTCATCACATCGGCCATTAGGC
*
39193 CTTATCACATATA-AC-ACTTTCACA-TCATGCACATCGGCTATTAGGC
1 CTTATCACATATATACAACTTTCACATTCAT-CACATCGGCCATTAGGC
* *
39239 CTTCATCA-ATATATAC-A-TTCCACA-TC--CACATCGGGCTATTAGGC
1 CTT-ATCACATATATACAACTTTCACATTCATCACATC-GGCCATTAGGC
39283 CTTATCACATATATAC-ACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACAACTTTCACATTCATCACATCGGCCATTAGGC
* *
39330 CTTATCACATATATACATACCTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-A-CTTTCACATTCATCACATCGGCCATTAGGC
39380 CTTATCACATATATACACACTTTCACATTCATACACATCGGCCATTAGGC
1 CTTATCACATATATACA-ACTTTCACATTCAT-CACATCGGCCATTAGGC
39430 CTTATCACATATATA
1 CTTATCACATATATA
39445 AATTCACATT
Statistics
Matches: 299, Mismatches: 21, Indels: 45
0.82 0.06 0.12
Matches are distributed among these distances:
43 10 0.03
44 35 0.12
45 41 0.14
46 39 0.13
47 49 0.16
48 34 0.11
49 15 0.05
50 76 0.25
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (48 bp):
CTTATCACATATATACAACTTTCACATTCATCACATCGGCCATTAGGC
Done.