Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2142
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: 36661
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:380 original size:19 final size:20
Alignment explanation
Indices: 339--380 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
329 TTGATCTTAA
*
339 TTAATAATAATTATTATATT
1 TTAATAATAATTATTATACT
*
359 TTAATAAT-ATTTTTATACT
1 TTAATAATAATTATTATACT
378 TTA
1 TTA
381 TTTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATAATAATTATTATACT
Found at i:4828 original size:154 final size:154
Alignment explanation
Indices: 4095--4828 Score: 453
Period size: 154 Copynumber: 4.8 Consensus size: 154
4085 AGTTTAGAAT
* * * * * * *
4095 GATGAACCTATTCCT-ACTGCACAGTATTGGCATAAAAGCAACCTGGTGACT-AGCTAGGACTTG
1 GATGAACCTA-TCCTAAATGCACACTTTTAGCATAAAAGCAACCCGGTGA-TGACCTAAGACTTG
* * * * * * * * *
4158 ATTCTAAAAAAATTATCAAAATGCCCATAAGATATACTTTCAATGTAAAAGTAATGC--GATAAC
64 ATT-TTAAAAAATTATAAAAATGCCCTTAGGGTATACCTTCAACGTGAAAGT-AT-CTTGGTAAC
** * * * *
4221 TTTAAAGGATATGAAAAGATCAATAAAAG
126 CCTAAAAGACATGAAAAGATTAGTAAAAG
* * * * * * * * ** * * *
4250 GATGAACCTATCATAAATGCACACCTCTAGTATAAAACCGACCCGATTAAAACCTCATACTTGGT
1 GATGAACCTATCCTAAATGCACACTTTTAGCATAAAAGCAACCCGGTGATGACCTAAGACTTGAT
* * * * * ** * * * * *
4315 TTAAAAAAATTATGAAAATACCC-TACGGTAAATTTTCGACTTAAAAGTATCTCGGTAACCTTAA
66 TTTAAAAAATTATAAAAATGCCCTTAGGGTATACCTTCAACGTGAAAGTATCTTGGTAACCCTAA
* * * *
4379 AGGACGA-AAAAAGA-TCGTTAATAG
131 AAGAC-ATGAAAAGATTAG-TAAAAG
* * * * *
4403 GATGAACCTATCCCAAATGCATA-TCTTAGGCATAAAAGCAA-CCGCGTGATGACCTAAAACTCG
1 GATGAACCTATCCTAAATGCACACTTTTA-GCATAAAAGCAACCCG-GTGATGACCTAAGACTTG
* * * * * **
4466 ATTTTAGAGAAATTATAAAAATGTCTTTAAGGTATACCTTCAACGTGAAAGTACCTTAATAACCC
64 ATTTTA-AAAAATTATAAAAATGCCCTTAGGGTATACCTTCAACGTGAAAGTATCTTGGTAACCC
* * * *
4531 TAAAACATAGGCAAAGATTAGTAAAAG
128 TAAAAGACATGAAAAGATTAGTAAAAG
* ** * * * * * * *
4558 AACAAACCTATCCTAAATGCACACATTTAACATAAAAGCGACCCAGTGAT-AACTTAGAATTCGA
1 GATGAACCTATCCTAAATGCACACTTTTAGCATAAAAGCAACCCGGTGATGACCTAAGACTT-GA
* * * ** * * * ** *
4622 TTCTAAGAAATTATTAAAATGCTTTTCGAGTATACTTTTGACGTGAACGTATCTTGGTAACCCTA
65 TTTTAAAAAATTATAAAAATGCCCTTAGGGTATACCTTCAACGTGAAAGTATCTTGGTAACCCTA
4687 AAAGACATGAAAAGATTAGTAAAAG
130 AAAGACATGAAAAGATTAGTAAAAG
* * * *
4712 GATGAACCTATCCTAAATGCACATTTTTAGTATAAAAGCAATCCGGTGATGACCTAAGACTTGGT
1 GATGAACCTATCCTAAATGCACACTTTTAGCATAAAAGCAACCCGGTGATGACCTAAGACTTGAT
* *
4777 TTTAAAAAATTATAAAAATGCCCTTGGGGTATACCTTCAACATGAAAGTATC
66 TTTAAAAAATTATAAAAATGCCCTTAGGGTATACCTTCAACGTGAAAGTATC
4829 CTAGTATTCC
Statistics
Matches: 426, Mismatches: 137, Indels: 33
0.71 0.23 0.06
Matches are distributed among these distances:
151 1 0.00
152 7 0.02
153 86 0.20
154 195 0.46
155 130 0.31
156 7 0.02
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (154 bp):
GATGAACCTATCCTAAATGCACACTTTTAGCATAAAAGCAACCCGGTGATGACCTAAGACTTGAT
TTTAAAAAATTATAAAAATGCCCTTAGGGTATACCTTCAACGTGAAAGTATCTTGGTAACCCTAA
AAGACATGAAAAGATTAGTAAAAG
Found at i:6302 original size:16 final size:14
Alignment explanation
Indices: 6264--6297 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6254 GGCTTTTTCC
* *
6264 TTTATTTTTCTTTT
1 TTTATTTATGTTTT
6278 TTTATTTATGTTTT
1 TTTATTTATGTTTT
6292 TTTATT
1 TTTATT
6298 GTTATTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTATTTATGTTTT
Found at i:8352 original size:33 final size:33
Alignment explanation
Indices: 8315--8381 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8305 TTCAACGATT
8315 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
8348 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
8381 T
1 T
8382 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:8353 original size:13 final size:13
Alignment explanation
Indices: 8335--8359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8325 CATAAAATGT
8335 TGTATCGATACAA
1 TGTATCGATACAA
8348 TGTATCGATACA
1 TGTATCGATACA
8360 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:8443 original size:13 final size:13
Alignment explanation
Indices: 8425--8449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8415 ATTACTCACA
8425 TGTATCGATACAT
1 TGTATCGATACAT
8438 TGTATCGATACA
1 TGTATCGATACA
8450 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8514 original size:52 final size:52
Alignment explanation
Indices: 8458--8578 Score: 233
Period size: 52 Copynumber: 2.3 Consensus size: 52
8448 CACTGATCTT
8458 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
8510 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
8562 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
8579 TAACTCTTCA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:14271 original size:22 final size:21
Alignment explanation
Indices: 14218--14273 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
14208 CTATGAATAT
*
14218 TTATGCACTAAAATTGGACAC
1 TTATGTACTAAAATTGGACAC
*
14239 TTATGTACTAACATTGGACAC
1 TTATGTACTAAAATTGGACAC
*
14260 TTAATGTCCTAAAA
1 TT-ATGTACTAAAA
14274 AATTCTATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (21 bp):
TTATGTACTAAAATTGGACAC
Found at i:16217 original size:25 final size:24
Alignment explanation
Indices: 16165--16209 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16155 TCTTAGTGTG
*
16165 AAACCTTTTTCATTATTAATGTTA
1 AAACATTTTTCATTATTAATGTTA
*
16189 AAACATTTTTTATT-TTAATGT
1 AAACATTTTTCATTATTAATGT
16210 ATTAAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.53
Consensus pattern (24 bp):
AAACATTTTTCATTATTAATGTTA
Found at i:24129 original size:52 final size:51
Alignment explanation
Indices: 24051--24199 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
24041 CGAAATATGA
24051 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
24103 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
24155 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
24200 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:24280 original size:20 final size:20
Alignment explanation
Indices: 24251--24308 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
24241 GCAGTAGCTT
24251 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
24270 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
24290 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
24309 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:25272 original size:48 final size:47
Alignment explanation
Indices: 25070--25297 Score: 234
Period size: 48 Copynumber: 4.8 Consensus size: 47
25060 AAAAGGATGT
* * *
25070 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-GG--AAGGTGC
*
25122 CAA-ATGCTGATTCAAGGCCAGCTATATTGGACTT-----AAGGTGT
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGAAGGTGC
* * * *
25163 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-AGGAAGGTGC
* *
25212 CAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGGCAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGG-AAGGTGC
* *
25260 CAATATGCTGATTTAAGGCCAGCTATATTGGGCTTAAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
25298 AGGAGACGCC
Statistics
Matches: 151, Mismatches: 16, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
41 9 0.06
42 28 0.19
47 2 0.01
48 45 0.30
49 36 0.24
51 28 0.19
52 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (47 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGAAGGTGC
Found at i:25297 original size:97 final size:92
Alignment explanation
Indices: 25070--25297 Score: 280
Period size: 97 Copynumber: 2.4 Consensus size: 92
25060 AAAAGGATGT
*
25070 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAATGCTGATTC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGTGCCAAATGCTGATTC
* *
25135 AAGGCCAGCTATATTGGACTTAAGGTGT
65 AAGGCCAGCGATATTGGACTTAAGGTGC
* * *
25163 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G-AAGGTGCCAATATGCTGATTT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAA-ATGCTGATTC
25226 AAGGCCAGCGATATTGGACTTAAAGGCAAGGTGC
65 AAGGCCAGCGATATTGGACTT------AAGGTGC
* * * *
25260 CAATATGCTGATTTAAGGCCAGCTATATTGGGCTTAAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
25298 AGGAGACGCC
Statistics
Matches: 117, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
90 10 0.09
91 29 0.25
92 1 0.01
93 38 0.32
97 39 0.33
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAAATGCTGATTCA
AGGCCAGCGATATTGGACTTAAGGTGC
Found at i:25400 original size:30 final size:30
Alignment explanation
Indices: 25341--25659 Score: 312
Period size: 30 Copynumber: 10.7 Consensus size: 30
25331 AGGTTTGCAT
*
25341 CACTGACTTGTGGGCTTTT--AAAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
25369 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
25399 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
25429 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* ** *
25459 CACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGC
1 CACTGACTTGTGGGCTT---TTG-AAAAGGGTGC
* * * * *
25493 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGC
1 CACT-GACTTGTGGGCTTTTGAAAAGGGTGC
* ***
25522 CACCGACTTGTGGGCTTCAAAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* *
25552 CACTGATTTGTGGGC-TTTG--AAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
***
25579 CACTGACTTGTGGGCTTTTGAAAAAAATGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
***
25609 CACTGACTTGTGGGC-TTTGAAAAATATGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
25638 CACTGACTTGTGGACTTTTGAA
1 CACTGACTTGTGGGCTTTTGAA
25660 GGGTGATAAA
Statistics
Matches: 245, Mismatches: 33, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
27 21 0.09
28 23 0.09
29 47 0.19
30 131 0.53
31 1 0.00
33 2 0.01
34 20 0.08
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (30 bp):
CACTGACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:25603 original size:123 final size:123
Alignment explanation
Indices: 25376--25595 Score: 302
Period size: 123 Copynumber: 1.8 Consensus size: 123
25366 TGCCACTGAC
* * * * ***
25376 TTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTG
1 TTGTGAGCTTTGGAAAAGGATGCCACCAACTTGTGGGCTTCAAAAAAGGGTGCCACTAACTTGTG
25441 GGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGCTATAGAG
66 GGCTTTTG-AAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGCTATAGAG
* * *
25500 TTGTGAGCTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCAAAAAAGGGTGCCACTGATTTGTG
1 TTGTGAGCTTTGGAAAAGGATGCCACCAACTTGTGGGCTTCAAAAAAGGGTGCCACTAACTTGTG
* *
25564 GGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTT
66 GGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTT
25596 TTGAAAAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
120 23 0.27
122 4 0.05
123 42 0.50
124 15 0.18
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.29
Consensus pattern (123 bp):
TTGTGAGCTTTGGAAAAGGATGCCACCAACTTGTGGGCTTCAAAAAAGGGTGCCACTAACTTGTG
GGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGCTATAGAG
Found at i:27102 original size:1 final size:1
Alignment explanation
Indices: 27098--27229 Score: 111
Period size: 1 Copynumber: 132.0 Consensus size: 1
27088 TCGGACCCCC
* * * * * * * *
27098 TTTTTTTGTTTTTGTTTATTTTTTTTTGTTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** ** * * * *
27163 TTTTTTTTTTGTTTTTTCATTTTTTTCGTTTTTTTTTTGTTTTGTTTTGTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27228 TT
1 TT
27230 GGAGGACGCC
Statistics
Matches: 99, Mismatches: 32, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 99 1.00
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (1 bp):
T
Found at i:27121 original size:20 final size:20
Alignment explanation
Indices: 27098--27230 Score: 146
Period size: 21 Copynumber: 6.4 Consensus size: 20
27088 TCGGACCCCC
*
27098 TTTTTTTGTTTTTGTTTATT
1 TTTTTTTGTTTTTGTTTTTT
27118 TTTTTTTGTTTTTGTTTTTT
1 TTTTTTTGTTTTTGTTTTTT
27138 TTTGTTTT-TTTTTGTTTTTTT
1 TTT-TTTTGTTTTTG-TTTTTT
*
27159 TTTGTTTTTTTTTTGTTTTTT
1 TTT-TTTTGTTTTTGTTTTTT
27180 CATTTTTTTCGTTTTT-TTTTTGT
1 --TTTTTTT-GTTTTTGTTTTT-T
*
27203 TTTGTTTTGTTTTT-TTTTTG
1 TTT-TTTTGTTTTTGTTTTTT
27223 TTTTTTTG
1 TTTTTTTG
27231 GAGGACGCCG
Statistics
Matches: 102, Mismatches: 3, Indels: 17
0.84 0.02 0.14
Matches are distributed among these distances:
19 5 0.05
20 31 0.30
21 38 0.37
22 19 0.19
23 9 0.09
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (20 bp):
TTTTTTTGTTTTTGTTTTTT
Found at i:27129 original size:10 final size:10
Alignment explanation
Indices: 27101--27229 Score: 138
Period size: 10 Copynumber: 12.7 Consensus size: 10
27091 GACCCCCTTT
27101 TTTTGTTTTTG
1 TTTT-TTTTTG
27112 TTTATTTTTT-
1 TTT-TTTTTTG
*
27122 TTTGTTTTTG
1 TTTTTTTTTG
27132 TTTTTTTTTG
1 TTTTTTTTTG
27142 TTTTTTTTTG
1 TTTTTTTTTG
27152 TTTTTTTTT-
1 TTTTTTTTTG
27161 TGTTTTTTTT-
1 T-TTTTTTTTG
* *
27171 TTGTTTTTTC
1 TTTTTTTTTG
* *
27181 ATTTTTTTCG
1 TTTTTTTTTG
27191 TTTTTTTTTTG
1 -TTTTTTTTTG
*
27202 TTTTGTTTTG
1 TTTTTTTTTG
27212 TTTTTTTTTTG
1 -TTTTTTTTTG
27223 TTTTTTT
1 TTTTTTT
27230 GGAGGACGCC
Statistics
Matches: 101, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
9 13 0.13
10 62 0.61
11 25 0.25
12 1 0.01
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:27130 original size:11 final size:11
Alignment explanation
Indices: 27098--27229 Score: 135
Period size: 11 Copynumber: 11.4 Consensus size: 11
27088 TCGGACCCCC
27098 TTTTTTTGTTT
1 TTTTTTTGTTT
27109 TTGTTTATT-TTT
1 TT-TTT-TTGTTT
*
27121 TTTTGTTTTTGTT
1 TTTT-TTTGT-TT
27134 TTTTTTTG-TT
1 TTTTTTTGTTT
27144 TTTTTTTGTTT
1 TTTTTTTGTTT
27155 TTTTTTTGTTT
1 TTTTTTTGTTT
27166 TTTTTTTGTTTTTT
1 TTTTTTTG---TTT
27180 CATTTTTTTCGTTT
1 --TTTTTTT-GTTT
27194 TTTTTTTG-TT
1 TTTTTTTGTTT
*
27204 TTGTTTTGTTT
1 TTTTTTTGTTT
27215 TTTTTTTGTTT
1 TTTTTTTGTTT
27226 TTTT
1 TTTT
27230 GGAGGACGCC
Statistics
Matches: 105, Mismatches: 3, Indels: 26
0.78 0.02 0.19
Matches are distributed among these distances:
10 19 0.18
11 44 0.42
12 20 0.19
13 8 0.08
14 6 0.06
16 7 0.07
17 1 0.01
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:27179 original size:49 final size:49
Alignment explanation
Indices: 27098--27228 Score: 173
Period size: 49 Copynumber: 2.7 Consensus size: 49
27088 TCGGACCCCC
* * *
27098 TTTTTTTG-TTTTTGTTT-ATTTTTTTTTGTTTTTGT--TTTTTTTTGTT
1 TTTTTTTGTTTTTTTTTTGTTTTTTTTTTGTTTTT-TCATTTTTTTCGTT
27144 TTTTTTTGTTTTTTTTTTGTTTTTTTTTTGTTTTTTCATTTTTTTCGTT
1 TTTTTTTGTTTTTTTTTTGTTTTTTTTTTGTTTTTTCATTTTTTTCGTT
*
27193 TTTTTTT-TGTTTTGTTTTGTTTTTTTTTTGTTTTTT
1 TTTTTTTGT-TTTTTTTTTGTTTTTTTTTTGTTTTTT
27229 TGGAGGACGC
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
46 8 0.11
47 9 0.12
48 16 0.21
49 43 0.57
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (49 bp):
TTTTTTTGTTTTTTTTTTGTTTTTTTTTTGTTTTTTCATTTTTTTCGTT
Done.