Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold924
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: 70277
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:2994 original size:2 final size:2
Alignment explanation
Indices: 2989--3017 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2979 TATATATATA
2989 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3018 ATTTTTACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3600 original size:20 final size:20
Alignment explanation
Indices: 3549--3600 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3539 TGGAGCAGAA
*
3549 ATATCGATACATTAGAAAAT
1 ATATCGATACCTTAGAAAAT
*
3569 ATATCGACACCTTAAGAAAA-
1 ATATCGATACCTT-AGAAAAT
*
3589 GTATCGATACCT
1 ATATCGATACCT
3601 ACCAAGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (20 bp):
ATATCGATACCTTAGAAAAT
Found at i:6243 original size:20 final size:21
Alignment explanation
Indices: 6218--6258 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6208 CATGATAATG
6218 TCAATGCA-AAATTTTAGAAA
1 TCAATGCATAAATTTTAGAAA
*
6238 TCAATGCATAATTTTTAGAAA
1 TCAATGCATAAATTTTAGAAA
6259 ACATTCCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (21 bp):
TCAATGCATAAATTTTAGAAA
Found at i:8044 original size:38 final size:38
Alignment explanation
Indices: 7999--8139 Score: 201
Period size: 38 Copynumber: 3.7 Consensus size: 38
7989 AAAGACCTGT
** *
7999 AGGCTTCGTGCTGAAAATATATCCGGGTTAAATCTCGC
1 AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
8037 AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
1 AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
* *
8075 AGGCTTCGTGCTGGTATTATATCCGGGATAAATCCCGC
1 AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
* * * *
8113 AGGCCTAGTGCTGGTATTATATTCGGG
1 AGGCTTCGTGCTGGTAATATATCCGGG
8140 CCTTTGAGCC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 95 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (38 bp):
AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
Found at i:8297 original size:45 final size:45
Alignment explanation
Indices: 8132--8305 Score: 237
Period size: 45 Copynumber: 3.9 Consensus size: 45
8122 GCTGGTATTA
* * * *
8132 TATTCGGGCCTTTGAGCCTAGCAAGCTATTATGCTGGTGAGACAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
* *
8177 TATTCAAGCCTTTGAGCCTAGCAGGCTATTATG-CGGTGAGACAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
* *
8221 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
8266 TATTCAGG-CTTTCGAGCCTAGCAGG-TCATAATGCCGGTGA
1 TATTCAGGCCTTT-GAGCCTAGCAGGCT-ATAATGCCGGTGA
8306 AATGATATCG
Statistics
Matches: 117, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
44 45 0.38
45 72 0.62
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (45 bp):
TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
Found at i:8320 original size:89 final size:89
Alignment explanation
Indices: 8132--8305 Score: 253
Period size: 89 Copynumber: 1.9 Consensus size: 89
8122 GCTGGTATTA
* * *
8132 TATTCGGGCCTTTGAGCCTAGCAAGCTATTATGCTGGTGAGACACTATTCAAGCCTTTGAGCCTA
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACACTATTCAAGCCTTTGAGCCTA
*
8197 GCAGGCTATTATGCGGTGAGACAC
66 GCAGGCTATAATGCGGTGAGACAC
* *
8221 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATACTATTC-AGGCTTTCGAGCCT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACACTATTCAAGCCTTT-GAGCCT
8285 AGCAGG-TCATAATGCCGGTGA
65 AGCAGGCT-ATAATG-CGGTGA
8306 AATGATATCG
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
88 7 0.09
89 63 0.83
90 6 0.08
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (89 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACACTATTCAAGCCTTTGAGCCTA
GCAGGCTATAATGCGGTGAGACAC
Found at i:12037 original size:37 final size:37
Alignment explanation
Indices: 11972--12117 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
11962 TACGTATGAT
* *
11972 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
12007 CACCTATCACTTTGTTTCTTGATCACATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
12044 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
12081 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
12118 TAAAGCTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 90 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:12134 original size:46 final size:46
Alignment explanation
Indices: 12081--12446 Score: 437
Period size: 52 Copynumber: 7.6 Consensus size: 46
12071 TAAGTGTAGC
* **
12081 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
12127 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
12173 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
12225 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
12277 CAC-TATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
12322 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
12368 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
12420 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
12447 AGTACTCAAA
Statistics
Matches: 289, Mismatches: 17, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
45 36 0.12
46 118 0.41
48 1 0.00
49 2 0.01
50 1 0.00
51 9 0.03
52 122 0.42
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:20407 original size:73 final size:74
Alignment explanation
Indices: 20281--20424 Score: 193
Period size: 73 Copynumber: 1.9 Consensus size: 74
20271 ATCAAAATCG
* * *
20281 ATGGTAACCAGATTTCTATCCCTCGAGACAATGACCCAATCTCCAATTGGTTAACAAGTTGCCTA
1 ATGGAAACCAGATTTCTAACCCTC-AGACAATGACCCAAGCTCCAATTGGTTAACAAGTTGCCTA
*
20346 TTGCATTGGT
65 TGGCATTGGT
* * *
20356 ATGGAAACTAGATTTCTAACCCTC-GACAATGGA-CCAAGCTTCGATTGGTTAACAAGTTGCCTA
1 ATGGAAACCAGATTTCTAACCCTCAGACAAT-GACCCAAGCTCCAATTGGTTAACAAGTTGCCTA
20419 TGGCAT
65 TGGCAT
20425 ATGTACAGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
73 38 0.62
74 2 0.03
75 21 0.34
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (74 bp):
ATGGAAACCAGATTTCTAACCCTCAGACAATGACCCAAGCTCCAATTGGTTAACAAGTTGCCTAT
GGCATTGGT
Found at i:25179 original size:17 final size:17
Alignment explanation
Indices: 25157--25191 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25147 TTTTAAAAAA
*
25157 TTTATGAATTTTTAAAT
1 TTTATGAAATTTTAAAT
*
25174 TTTATGAAATTTTGAAT
1 TTTATGAAATTTTAAAT
25191 T
1 T
25192 ATTTGTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (17 bp):
TTTATGAAATTTTAAAT
Found at i:30823 original size:12 final size:11
Alignment explanation
Indices: 30803--30832 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
30793 AAAAGTTTAC
30803 AATTTAATATT
1 AATTTAATATT
30814 AATATTAATATT
1 AAT-TTAATATT
30826 AATTTAA
1 AATTTAA
30833 ATTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTTAATATT
Found at i:33581 original size:18 final size:17
Alignment explanation
Indices: 33524--33582 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
33514 AAAGAAAATG
*
33524 AATATAATAAT-ACAAT
1 AATATAATAATGATAAT
*
33540 AATA-AATAGTGAT-AT
1 AATATAATAATGATAAT
33555 AATAATAATAATGATAAT
1 AAT-ATAATAATGATAAT
33573 AATGATAATA
1 AAT-ATAATA
33583 TAAGTAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 10 0.29
16 6 0.17
17 8 0.23
18 11 0.31
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (17 bp):
AATATAATAATGATAAT
Found at i:37322 original size:15 final size:15
Alignment explanation
Indices: 37273--37325 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
37263 ATTAAATTAA
37273 TAGGCGAACCCCCT-T
1 TAGGCGAA-CCCCTAT
* * *
37288 TATGTGAACTCCTA-
1 TAGGCGAACCCCTAT
37302 TAGGCGAACCCCTAT
1 TAGGCGAACCCCTAT
37317 TAGGCGAAC
1 TAGGCGAAC
37326 TGTAGTTGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 15 0.50
15 15 0.50
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (15 bp):
TAGGCGAACCCCTAT
Found at i:37454 original size:18 final size:18
Alignment explanation
Indices: 37428--37463 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
37418 ACCTTACATG
37428 TTTAACATGCGAACCCTA
1 TTTAACATGCGAACCCTA
* *
37446 TTTACCATGTGAACCCTA
1 TTTAACATGCGAACCCTA
37464 CCTATTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (18 bp):
TTTAACATGCGAACCCTA
Found at i:37522 original size:23 final size:22
Alignment explanation
Indices: 37442--37528 Score: 66
Period size: 23 Copynumber: 3.9 Consensus size: 22
37432 ACATGCGAAC
* *
37442 CCTATTTACCATGTGAACCCTA
1 CCTATTTAACATGTAAACCCTA
* * *
37464 CCTATTTAATATGCAAACCTTA
1 CCTATTTAACATGTAAACCCTA
* * *
37486 CATGTCTAAACATGTAAACCCTA
1 CCTAT-TTAACATGTAAACCCTA
* *
37509 CCTAGTTTACCATGTGAACC
1 CCTA-TTTAACATGTAAACC
37529 TCGCATGCTT
Statistics
Matches: 47, Mismatches: 16, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
22 20 0.43
23 26 0.55
24 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (22 bp):
CCTATTTAACATGTAAACCCTA
Found at i:37562 original size:14 final size:14
Alignment explanation
Indices: 37543--37582 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
37533 ATGCTTACTT
37543 GTGCAAACCTTTAA
1 GTGCAAACCTTTAA
*
37557 GTGCAAACTCTTTAT
1 GTGCAAAC-CTTTAA
*
37572 GTGCGAACCTT
1 GTGCAAACCTT
37583 GATGCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (14 bp):
GTGCAAACCTTTAA
Found at i:37575 original size:15 final size:14
Alignment explanation
Indices: 37542--37596 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
37532 CATGCTTACT
37542 TGTGCAAACCTTTA
1 TGTGCAAACCTTTA
*
37556 AGTGCAAACTCTTTA
1 TGTGCAAAC-CTTTA
* *
37571 TGTGCGAACCTTGA
1 TGTGCAAACCTTTA
37585 TGCATGCAAACC
1 TG--TGCAAACC
37597 CCCTATACAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 14 0.42
15 12 0.36
16 7 0.21
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (14 bp):
TGTGCAAACCTTTA
Found at i:40576 original size:26 final size:26
Alignment explanation
Indices: 40540--40649 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
40530 CATGAAATTC
40540 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
40566 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
40592 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* * *
40618 TTATCATGGAATATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
40644 TTATCA
1 TTATCA
40650 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:44031 original size:22 final size:22
Alignment explanation
Indices: 44006--44048 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43996 TATCTAAACA
44006 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
** *
44028 ATAATAATGAAATGGTAGCAA
1 ATAATAACAAAATAGTAGCAA
44049 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:44374 original size:21 final size:22
Alignment explanation
Indices: 44350--44406 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
44340 TATTTTTGTT
44350 GCTATATTTTTTTT-AATA-AGA
1 GCTATATTTTTTTTAAATAGA-A
*
44371 GCTA-ATATTTTTTAAATAGAA
1 GCTATATTTTTTTTAAATAGAA
44392 GCTAATATTTTTTTT
1 GCT-ATATTTTTTTT
44407 TATTTCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 8 0.27
21 12 0.40
22 2 0.07
23 8 0.27
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (22 bp):
GCTATATTTTTTTTAAATAGAA
Found at i:44383 original size:20 final size:21
Alignment explanation
Indices: 44357--44404 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
44347 GTTGCTATAT
*
44357 TTTTTTTAATA-AGAGCTAATA
1 TTTTTTAAATAGA-AGCTAATA
44378 TTTTTTAAATAGAAGCTAATA
1 TTTTTTAAATAGAAGCTAATA
44399 TTTTTT
1 TTTTTT
44405 TTTATTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (21 bp):
TTTTTTAAATAGAAGCTAATA
Found at i:48427 original size:20 final size:20
Alignment explanation
Indices: 48376--48427 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
48366 TGGAGCAGAA
*
48376 ATATCGATACATTAGAAAAT
1 ATATCGATACCTTAGAAAAT
*
48396 ATATCGACACCTTAAGAAAA-
1 ATATCGATACCTT-AGAAAAT
*
48416 GTATCGATACCT
1 ATATCGATACCT
48428 ACTAAGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (20 bp):
ATATCGATACCTTAGAAAAT
Found at i:51072 original size:20 final size:21
Alignment explanation
Indices: 51047--51087 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
51037 CATGATAATG
51047 TCAATGCA-AAATTTTAGAAA
1 TCAATGCATAAATTTTAGAAA
*
51067 TCAATGCATAATTTTTAGAAA
1 TCAATGCATAAATTTTAGAAA
51088 ACATTCCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (21 bp):
TCAATGCATAAATTTTAGAAA
Found at i:52874 original size:38 final size:38
Alignment explanation
Indices: 52829--52969 Score: 201
Period size: 38 Copynumber: 3.7 Consensus size: 38
52819 AAAGACCTGT
** *
52829 AGGCTTCGTGCTGAAAATATATCCGGGTTAAATCTCGC
1 AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
52867 AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
1 AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
* *
52905 AGGCTTCGTGCTGGTATTATATCCGGGATAAATCCCGC
1 AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
* * * *
52943 AGGCCTAGTGCTGGTATTATATTCGGG
1 AGGCTTCGTGCTGGTAATATATCCGGG
52970 CCTTTGAGCC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 95 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (38 bp):
AGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGC
Found at i:53128 original size:45 final size:45
Alignment explanation
Indices: 52962--53136 Score: 228
Period size: 45 Copynumber: 3.9 Consensus size: 45
52952 GCTGGTATTA
* * * *
52962 TATTCGGGCCTTTGAGCCTAGCAAGCTATTATGCTGGTGAGACAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
* * *
53007 TATTCAAGCCTTTGAGCCTAGCAGGCTATTATGTCGGTGAGACAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
* *
53052 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
*
53097 TATTCAGG-CTTTCGAGCCTAGCAGG-TCATAATACCGGTGA
1 TATTCAGGCCTTT-GAGCCTAGCAGGCT-ATAATGCCGGTGA
53137 AATGATATCG
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
44 5 0.04
45 111 0.96
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (45 bp):
TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
Found at i:62146 original size:73 final size:74
Alignment explanation
Indices: 62020--62163 Score: 193
Period size: 73 Copynumber: 1.9 Consensus size: 74
62010 ATCAAAATCG
* * *
62020 ATGGTAACCAGATTTCTATCCCTCGAGACAATGACCCAATCTCCAATTGGTTAACAAGTTGCCTA
1 ATGGAAACCAGATTTCTAACCCTC-AGACAATGACCCAAGCTCCAATTGGTTAACAAGTTGCCTA
*
62085 TTGCATTGGT
65 TGGCATTGGT
* * *
62095 ATGGAAACTAGATTTCTAACCCTC-GACAATGGA-CCAAGCTTCGATTGGTTAACAAGTTGCCTA
1 ATGGAAACCAGATTTCTAACCCTCAGACAAT-GACCCAAGCTCCAATTGGTTAACAAGTTGCCTA
62158 TGGCAT
65 TGGCAT
62164 ATGTACAGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
73 38 0.62
74 2 0.03
75 21 0.34
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (74 bp):
ATGGAAACCAGATTTCTAACCCTCAGACAATGACCCAAGCTCCAATTGGTTAACAAGTTGCCTAT
GGCATTGGT
Found at i:66904 original size:17 final size:17
Alignment explanation
Indices: 66882--66916 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
66872 TTTTAAAAAA
*
66882 TTTATGAATTTTTAAAT
1 TTTATGAAATTTTAAAT
*
66899 TTTATGAAATTTTGAAT
1 TTTATGAAATTTTAAAT
66916 T
1 T
66917 ATTTGTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (17 bp):
TTTATGAAATTTTAAAT
Done.