Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1894
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: 39191
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:6796 original size:40 final size:40
Alignment explanation
Indices: 6713--6929 Score: 278
Period size: 40 Copynumber: 5.4 Consensus size: 40
6703 ACCCAAGTAT
* * *
6713 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGT
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
6752 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
6792 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
6832 CTTCGGGACTTAGCCC-GAGTATAGACACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGA-TATAGTCACTA---GCACAAATGC
* * *
6875 CTTCGGGACTGAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
6915 CTTCGGGACTTAGCC
1 CTTCGGGACTTAGCC
6930 GAGATATCAT
Statistics
Matches: 156, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
39 13 0.08
40 107 0.69
41 1 0.01
43 33 0.21
44 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:6910 original size:83 final size:80
Alignment explanation
Indices: 6713--6929 Score: 285
Period size: 83 Copynumber: 2.7 Consensus size: 80
6703 ACCCAAGTAT
* * * * * *
6713 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGTCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGA
**
6777 CACTAGCATGAATGC
66 CACTAGCACAAATGC
*
6792 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC-GAGTATAG
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGA-TATAG
6856 ACACTACTCGCACAAATGC
65 ACACTA---GCACAAATGC
* *
6875 CTTCGGGACTGAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCC
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCC
6930 GAGATATCAT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
79 14 0.12
80 47 0.39
83 60 0.50
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGA
CACTAGCACAAATGC
Found at i:12274 original size:21 final size:20
Alignment explanation
Indices: 12246--12289 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
12236 GATCTATACG
*
12246 AGTAAATT-TAACATCAATTT
1 AGTAAATTGAAAC-TCAATTT
12266 AGTACAATTGAAACTCAATTT
1 AGTA-AATTGAAACTCAATTT
12287 AGT
1 AGT
12290 CCAAATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 14 0.67
22 3 0.14
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (20 bp):
AGTAAATTGAAACTCAATTT
Found at i:20764 original size:31 final size:31
Alignment explanation
Indices: 20721--20799 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
20711 TTTAACGGTT
*
20721 ACTGGGCTGAAGCCTTTTCATAAATCAAATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
*
20752 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
20783 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
20800 ATTGTAAACG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCAAATC
Found at i:21049 original size:26 final size:26
Alignment explanation
Indices: 21017--21139 Score: 169
Period size: 26 Copynumber: 4.8 Consensus size: 26
21007 CCTCTTTAAT
**
21017 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
21042 AACTTGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
**
21067 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
* *
21093 AACTAGGGCATAAGCCCTTTTTAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
21119 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
21140 GCACTTCCTC
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 31 0.36
26 55 0.64
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:21128 original size:52 final size:51
Alignment explanation
Indices: 21011--21139 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 51
21001 GCCTAGCCTC
*
21011 TTTAAT-AACTGGGGCA-AAGCCCTTTTCGGTAAACTTGGGCAAAGCCCTT
1 TTTAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCAAAGCCCTT
*
21060 TTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCATAAGCCCTT
1 TTTAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCA-AAGCCCTT
21112 TTTAATAAACTGGGGCATAAGCCCTTTT
1 TTTAATAAACTGGGGCATAAGCCCTTTT
21140 GCACTTCCTC
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
49 5 0.07
50 10 0.14
51 24 0.32
52 35 0.47
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (51 bp):
TTTAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCAAAGCCCTT
Found at i:21223 original size:11 final size:11
Alignment explanation
Indices: 21207--21244 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
21197 CATTGCATAG
21207 ATATCATGTGC
1 ATATCATGTGC
21218 ATATCA--TGC
1 ATATCATGTGC
21227 ATATCATGTGC
1 ATATCATGTGC
21238 ATATCAT
1 ATATCAT
21245 ATCAATCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
11 16 0.64
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (11 bp):
ATATCATGTGC
Found at i:21255 original size:20 final size:20
Alignment explanation
Indices: 21189--21244 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
21179 TTATGAATTC
21189 ATCATGTGCAT-TGCATAG-AT
1 ATCATGTGCATAT-CAT-GCAT
21209 ATCATGTGCATATCATGCAT
1 ATCATGTGCATATCATGCAT
21229 ATCATGTGCATATCAT
1 ATCATGTGCATATCAT
21245 ATCAATCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATGCAT
Found at i:21319 original size:25 final size:25
Alignment explanation
Indices: 21291--21338 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21281 ATAATTAAAC
* * *
21291 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
21316 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
21339 CACATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:22012 original size:26 final size:26
Alignment explanation
Indices: 21946--22047 Score: 80
Period size: 27 Copynumber: 3.8 Consensus size: 26
21936 AGGTATATTC
21946 GTCATTTTACCATACAAGGGTATTACG
1 GTCATTTTACC-TACAAGGGTATTACG
* *
21973 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTA-CCTACAAGGG-TATTACG
* * ***
22000 GTCTTTTTACCTATTAAGGGTATTGTA
1 GTCATTTTACCTA-CAAGGGTATTACG
*
22027 GTCATTTCATCCTACAAGGGT
1 GTCATTTTA-CCTACAAGGGT
22048 GTTTTGGTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
26 5 0.09
27 46 0.79
28 7 0.12
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (26 bp):
GTCATTTTACCTACAAGGGTATTACG
Found at i:22094 original size:27 final size:27
Alignment explanation
Indices: 22064--22373 Score: 112
Period size: 27 Copynumber: 11.4 Consensus size: 27
22054 GTAAATCTAC
*
22064 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *
22091 AAACTAATGGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTTC-AGTAA-TTTTAT
* * *
22119 AAAGTCAAGGGTATTTCTA-TAAATTTGT
1 AAA-CCAAGGGTATTTC-AGTAATTTTAT
** * ** *
22147 AAATTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
*** * *
22174 AAATTGAGGGTATTTCGGTAATTTCAT
1 AAACCAAGGGTATTTCAGTAATTTTAT
** * *
22201 AAACC-AGTGGTATTTTGGTAACTTTAC
1 AAACCAAG-GGTATTTCAGTAATTTTAT
* * * *
22228 AAACTAGGGGTACTTT-GGTAATTTTAC
1 AAACCAAGGGTA-TTTCAGTAATTTTAT
* * * *
22255 AAACCAGGGGTATTTTAGCAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
22282 AGA-CTAGGGTATTTTC-GTAATTTTACT
1 AAACCAAGGGTA-TTTCAGTAATTTTA-T
* * * ** *
22309 -GATCGAGGGTATTTTGGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *
22335 AAACCAAAGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
22362 AAATCGAGGGTA
1 AAACCAAGGGTA
22374 AAATAGTAAT
Statistics
Matches: 219, Mismatches: 51, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
26 25 0.11
27 161 0.74
28 18 0.08
29 15 0.07
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTAT
Found at i:22213 original size:54 final size:53
Alignment explanation
Indices: 22154--22332 Score: 193
Period size: 54 Copynumber: 3.3 Consensus size: 53
22144 TGTAAATTAG
* *
22154 GGGTATTTTGGTAATTTTACAAATTGAGGGTA-TTTCGGTAATTTCATAAACCA
1 GGGTATTTTGGTAATTTTACAAACT-AGGGTACTTTCGGTAATTTTATAAACCA
* *
22207 GTGGTATTTTGGTAACTTTACAAACTAGGGGTACTTT-GGTAATTTTACAAACCA
1 G-GGTATTTTGGTAATTTTACAAACTA-GGGTACTTTCGGTAATTTTATAAACCA
* * * * * * *
22261 GGGGTATTTTAGCAATTTTACAGACTAGGGTATTTTC-GTAATTTTACTGATCGA
1 -GGGTATTTTGGTAATTTTACAAACTAGGGTACTTTCGGTAATTTTA-TAAACCA
22315 GGGTATTTTGGTAATTTT
1 GGGTATTTTGGTAATTTT
22333 GTAAACCAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
53 35 0.33
54 66 0.63
55 4 0.04
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTACAAACTAGGGTACTTTCGGTAATTTTATAAACCA
Found at i:22380 original size:27 final size:27
Alignment explanation
Indices: 22352--22641 Score: 409
Period size: 27 Copynumber: 10.7 Consensus size: 27
22342 AGGTATTTTA
* **
22352 GTAATTTTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
** * *
22379 GTAATTCTACAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
22406 GTAATTCTGTAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
22433 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
22460 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
22487 ATAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
22514 GTAATTTTGAAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
22541 GTAATTTTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
22568 GTAATTCTGTAAATCGAGGATAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
22595 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
**
22622 GTAATTCTACAAATCGAGGG
1 GTAATTCTGTAAATCGAGGG
22642 CATTTCAGTA
Statistics
Matches: 241, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 241 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:22383 original size:134 final size:134
Alignment explanation
Indices: 22154--22400 Score: 289
Period size: 134 Copynumber: 1.8 Consensus size: 134
22144 TGTAAATTAG
* * ** *
22154 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCATAAACCAGTGGTATTTTGG
1 GGGTATTTTCGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCATAAACCAAAGGTATTTTAG
* *** * * *
22219 TAACTTTACAAACTAGGGGTACTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTACAG
66 TAACTTTACAAACGAGGGGTAAAATAGTAATTCTACAAACCAAGGGTATTTTAGCAATTTTACAG
22284 ACTA
131 ACTA
** * **
22288 GGGTATTTTCGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAAGGTATTTTAG
1 GGGTATTTTCGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCATAAACCAAAGGTATTTTAG
* ** *
22353 TAATTTTGTAAATCGA-GGGTAAAATAGTAATTCTACAAATCAAGGGTA
66 TAACTTTACAAA-CGAGGGGTAAAATAGTAATTCTACAAACCAAGGGTA
22401 AAATGGTAAT
Statistics
Matches: 91, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
134 89 0.98
135 2 0.02
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (134 bp):
GGGTATTTTCGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCATAAACCAAAGGTATTTTAG
TAACTTTACAAACGAGGGGTAAAATAGTAATTCTACAAACCAAGGGTATTTTAGCAATTTTACAG
ACTA
Found at i:24803 original size:19 final size:20
Alignment explanation
Indices: 24764--24803 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
24754 AGACTTGTAT
24764 ATCTATCAACAAACATTCAA
1 ATCTATCAACAAACATTCAA
*
24784 ATCTATCAAGAAAC-TTCAA
1 ATCTATCAACAAACATTCAA
24803 A
1 A
24804 ACACATGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.50, C:0.23, G:0.03, T:0.25
Consensus pattern (20 bp):
ATCTATCAACAAACATTCAA
Found at i:29638 original size:27 final size:27
Alignment explanation
Indices: 29607--29784 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29597 TAAATTGTAC
29607 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
29634 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29660 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
29688 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
29716 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29743 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29770 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29785 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29721 original size:82 final size:81
Alignment explanation
Indices: 29608--29763 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29598 AAATTGTACA
* *
29608 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29672 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29689 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29754 TGCGAGTTGA
65 TGCGAATTGA
29764 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29775 original size:82 final size:81
Alignment explanation
Indices: 29604--29784 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
29594 GATTAAATTG
* *
29604 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29669 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
29685 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29749 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29767 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29785 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:37773 original size:27 final size:27
Alignment explanation
Indices: 37714--37890 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
37704 TAAATTGTAC
37714 AGCACTAAGTGT-CGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
37740 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
37766 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
37794 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
37822 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
37849 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
37876 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
37891 GACTCAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
26 11 0.09
27 94 0.73
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:37827 original size:82 final size:80
Alignment explanation
Indices: 37715--37869 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 80
37705 AAATTGTACA
* *
37715 GCACTAAGTGTCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGT
1 GCACTAAGTGTCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGT
37779 GCGAATTGACCATGCG
65 GCGAATTGACCATGCG
** *
37795 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGT-CGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
37860 TGCGAGTTGA
64 TGCGAATTGA
37870 TTATATAGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 11 0.17
81 3 0.05
82 51 0.77
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (80 bp):
GCACTAAGTGTCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTG
CGAATTGACCATGCG
Found at i:37881 original size:82 final size:81
Alignment explanation
Indices: 37711--37890 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
37701 GATTAAATTG
* *
37711 TACAGCACTAAGTGT-CGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
37775 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
37791 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
37855 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
37873 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
37891 GACTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 13 0.16
81 4 0.05
82 66 0.80
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.