Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold674
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: 41320
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:545 original size:28 final size:29
Alignment explanation
Indices: 454--617 Score: 170
Period size: 29 Copynumber: 5.7 Consensus size: 29
444 TATTAAATCC
**
454 CTAAACTTTTCAAAATTACACTTTGATTT
1 CTAAACTTTTCAAAATTACACTTTGACCT
* * * *
483 ATAAACATTTCAAAATTAAACATTGACC-
1 CTAAACTTTTCAAAATTACACTTTGACCT
511 CTTAAACTTTTCAAAATTACAC-TTGACCT
1 C-TAAACTTTTCAAAATTACACTTTGACCT
* * *
540 CTAAACTTATCAAAATTACGCTTTGACTT
1 CTAAACTTTTCAAAATTACACTTTGACCT
** *
569 CTAACACTTTTCAAAATTACGTTTTGACCC
1 CTAA-ACTTTTCAAAATTACACTTTGACCT
* *
599 CTCAACTTTCCAAAATTAC
1 CTAAACTTTTCAAAATTAC
618 CTGTTAACCT
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
28 24 0.21
29 65 0.58
30 24 0.21
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
CTAAACTTTTCAAAATTACACTTTGACCT
Found at i:2075 original size:2 final size:2
Alignment explanation
Indices: 2068--2104 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2058 GTTAAAAGCT
2068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2105 TATTAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2302 original size:5 final size:5
Alignment explanation
Indices: 2292--2317 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2282 AAACTAGTTA
2292 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
2318 TTCAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2343 original size:17 final size:18
Alignment explanation
Indices: 2314--2347 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2304 AATAAAATAA
2314 AATATTCAAAATTAAAAG
1 AATATTCAAAATTAAAAG
2332 AATATT-AAAATTAAAA
1 AATATTCAAAATTAAAA
2348 TTAATAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AATATTCAAAATTAAAAG
Found at i:2344 original size:6 final size:6
Alignment explanation
Indices: 2289--2351 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
2279 ATGAAACTAG
* * * *
2289 TTAAAA ATAAAA -TAAAA -TAAAA TAAAATA TTCAAAA TTAAAA -GAATA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAA-A TT-AAAA TTAAAA TTAAAA
2336 TTAAAA TTAAAA TTAA
1 TTAAAA TTAAAA TTAA
2352 TAATCATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
5 13 0.28
6 25 0.54
7 5 0.11
8 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (6 bp):
TTAAAA
Found at i:2353 original size:18 final size:18
Alignment explanation
Indices: 2292--2353 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 18
2282 AAACTAGTTA
2292 AAAATAAA-A-TAAAA-T
1 AAAATAAATATTAAAATT
2307 AAAATAAAATATTCAAAATT
1 AAAAT-AAATATT-AAAATT
*
2327 AAAA-GAATATTAAAATT
1 AAAATAAATATTAAAATT
*
2344 AAAATTAATA
1 AAAATAAATA
2354 ATCATAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 5 0.13
16 3 0.08
17 11 0.28
18 11 0.28
19 4 0.10
20 5 0.13
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAATAAATATTAAAATT
Found at i:5056 original size:15 final size:16
Alignment explanation
Indices: 5025--5058 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5015 ATAACTTTGA
*
5025 CTCCTTTGTTCTCTTC
1 CTCCTTTATTCTCTTC
5041 CTCCTTTATT-TCTTC
1 CTCCTTTATTCTCTTC
5056 CTC
1 CTC
5059 TTAACCTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.03, C:0.38, G:0.03, T:0.56
Consensus pattern (16 bp):
CTCCTTTATTCTCTTC
Found at i:9157 original size:42 final size:42
Alignment explanation
Indices: 9060--9176 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
9050 TTCTTTTTCA
*** *
9060 ACATTCACAAGATATGTGAAAAATCTTCTAAAACAAGATTTGC
1 ACATTCACAAGATACACG-AAAATCTTCTAAAACAAGATTTAC
* *
9103 ACGTTCACAAGATACGA-GAAAATCTTTTAAAACAAGATTTAC
1 ACATTCACAAGATAC-ACGAAAATCTTCTAAAACAAGATTTAC
* * *
9145 ATATTCATAAGATACACGAATATCTTCTAAAA
1 ACATTCACAAGATACACGAAAATCTTCTAAAA
9177 TAATTTTTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 47 0.76
43 14 0.23
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.28
Consensus pattern (42 bp):
ACATTCACAAGATACACGAAAATCTTCTAAAACAAGATTTAC
Found at i:12116 original size:2 final size:2
Alignment explanation
Indices: 12111--12138 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12101 ATGCAAAAAA
12111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12139 TATTAAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13215 original size:17 final size:16
Alignment explanation
Indices: 13195--13255 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
13185 TATTGTGGTG
* *
13195 TTATCATTATTATTATT
1 TTATAATTATAATT-TT
13212 TTATAATTATAATTTT
1 TTATAATTATAATTTT
*
13228 TTAATAATTA-ATATTTA
1 TT-ATAATTATA-ATTTT
13245 TTATTAATTAT
1 TTA-TAATTAT
13256 TTTTATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.16
17 31 0.84
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATAATTATAATTTT
Found at i:13226 original size:14 final size:15
Alignment explanation
Indices: 13203--13266 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 15
13193 TGTTATCATT
13203 ATTATT-ATTTTATA
1 ATTATTAATTTTATA
*
13217 ATTA-TAATTTTTTA
1 ATTATTAATTTTATA
* *
13231 ATAATTAATATTTATT
1 ATTATTAAT-TTTATA
*
13247 ATTAATTATTTTTATA
1 ATT-ATTAATTTTATA
13263 ATTA
1 ATTA
13267 ATTATAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
13 1 0.03
14 14 0.36
15 5 0.13
16 14 0.36
17 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATTAATTTTATA
Found at i:13246 original size:38 final size:36
Alignment explanation
Indices: 13204--13306 Score: 100
Period size: 38 Copynumber: 2.7 Consensus size: 36
13194 GTTATCATTA
** *
13204 TTATTATTTTATAATTATAATTTTTTAATAATTAATAT
1 TTATTATTTTATAATTATAATTAATT-ATAA-AAATAT
**
13242 TTATTATTAATTATTTTTATAATTAATTATAAAAATAT
1 TTATTATT--TTATAATTATAATTAATTATAAAAATAT
13280 TTATTATGTTTATAATTA-AATATAATT
1 TTATTAT-TTTATAATTATAAT-TAATT
13307 TAATTGATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
36 3 0.06
37 12 0.22
38 20 0.37
39 5 0.09
40 14 0.26
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (36 bp):
TTATTATTTTATAATTATAATTAATTATAAAAATAT
Found at i:13266 original size:16 final size:16
Alignment explanation
Indices: 13206--13271 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 16
13196 TATCATTATT
13206 ATTA-TTTTATAATT-
1 ATTATTTTTATAATTA
*
13220 ATAATTTTT-TAA-TA
1 ATTATTTTTATAATTA
* *
13234 ATTAATATTTATTATTA
1 ATT-ATTTTTATAATTA
13251 ATTATTTTTATAATTA
1 ATTATTTTTATAATTA
13267 ATTAT
1 ATTAT
13272 AAAAATATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 1 0.02
14 8 0.20
15 9 0.22
16 18 0.44
17 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTTTTATAATTA
Found at i:13286 original size:31 final size:31
Alignment explanation
Indices: 13246--13304 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
13236 TAATATTTAT
* *
13246 TATTAATTATTTTTATAATTAATTATAAAAA
1 TATTAATTATGTTTATAATTAAATATAAAAA
*
13277 TATTTATTATGTTTATAATTAAATATAA
1 TATTAATTATGTTTATAATTAAATATAA
13305 TTTAATTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (31 bp):
TATTAATTATGTTTATAATTAAATATAAAAA
Found at i:15164 original size:39 final size:38
Alignment explanation
Indices: 15100--15175 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
15090 AACAATGGAC
15100 ATGTGATCTCTGAGTTTATTTTTATATAATATTTTGAA
1 ATGTGATCTCTGAGTTTATTTTTATATAATATTTTGAA
* * **
15138 ATGTGATTTCTGATTTTTATTTTTATATTGTATTTTGA
1 ATGTGATCTCTGA-GTTTATTTTTATATAATATTTTGA
15176 GGCTATTGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 12 0.36
39 21 0.64
ACGTcount: A:0.25, C:0.04, G:0.13, T:0.58
Consensus pattern (38 bp):
ATGTGATCTCTGAGTTTATTTTTATATAATATTTTGAA
Found at i:15378 original size:19 final size:18
Alignment explanation
Indices: 15356--15392 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
15346 TTATTTATTA
15356 TAATTAATTATGATAATAT
1 TAATTAATTATG-TAATAT
15375 TAATTAATTATGTAATAT
1 TAATTAATTATGTAATAT
15393 ATTCATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
TAATTAATTATGTAATAT
Found at i:16142 original size:28 final size:27
Alignment explanation
Indices: 16078--16153 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 27
16068 TCAATTGTAC
* *
16078 TAATAATT-TTAAATTAGATATAAACA
1 TAATAATTATTAAATAAAATATAAACA
16104 TAATAA--A-TAAATAAAATATAATACA
1 TAATAATTATTAAATAAAATATAA-ACA
* *
16129 TAATAATTATTAAAAAAAATTTAAA
1 TAATAATTATTAAATAAAATATAAA
16154 AAATTGCCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
24 12 0.29
25 9 0.22
26 6 0.15
27 2 0.05
28 12 0.29
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (27 bp):
TAATAATTATTAAATAAAATATAAACA
Found at i:17480 original size:40 final size:41
Alignment explanation
Indices: 17411--17488 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
17401 AAGTTTAAAA
17411 ATTCGATTGATAGTTGAAAAGACTGAAATAAAAATACTTTG
1 ATTCGATTGATAGTTGAAAAGACTGAAATAAAAATACTTTG
* *
17452 ATTCGATTGATA-TTTAAAAGACTTAAATAAAAATACT
1 ATTCGATTGATAGTTGAAAAGACTGAAATAAAAATACT
17489 ATATTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 23 0.66
41 12 0.34
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (41 bp):
ATTCGATTGATAGTTGAAAAGACTGAAATAAAAATACTTTG
Found at i:18401 original size:45 final size:45
Alignment explanation
Indices: 18332--18422 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
18322 GTTTTACCTC
* * *
18332 TATGAATGTAAATTGTTCATGAAATGCCAAATAAGGATGGAAGTG
1 TATGAATGTAAATCGTTCAGGAAATGCCAAACAAGGATGGAAGTG
* * **
18377 TATGAATTTAAATCGTTTAGGAAATGTGAAACAAGGATGGAAGTG
1 TATGAATGTAAATCGTTCAGGAAATGCCAAACAAGGATGGAAGTG
18422 T
1 T
18423 GGTTAGAACT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (45 bp):
TATGAATGTAAATCGTTCAGGAAATGCCAAACAAGGATGGAAGTG
Found at i:21111 original size:24 final size:24
Alignment explanation
Indices: 21084--21157 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
21074 GGTGGGTGGC
21084 TTATTTAGTCAACAAAAGCCACCT
1 TTATTTAGTCAACAAAAGCCACCT
* **
21108 TTATTGATGTCAA-AAAAGGTGA-CT
1 TTATTTA-GTCAACAAAA-GCCACCT
* *
21132 CTCTTTAGTCAACAAAAGCCATCCT
1 TTATTTAGTCAACAAAAGCCA-CCT
21157 T
1 T
21158 ATTAGTATCA
Statistics
Matches: 36, Mismatches: 9, Indels: 9
0.67 0.17 0.17
Matches are distributed among these distances:
23 7 0.19
24 20 0.56
25 9 0.25
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (24 bp):
TTATTTAGTCAACAAAAGCCACCT
Found at i:27297 original size:32 final size:32
Alignment explanation
Indices: 27261--27325 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
27251 CAATTGCCTA
27261 TTAGCGAGACCATGGATACATTCAGCCGGGGC
1 TTAGCGAGACCATGGATACATTCAGCCGGGGC
27293 TTAGCGAGACCATGGATACATTCAGCCGGGGC
1 TTAGCGAGACCATGGATACATTCAGCCGGGGC
27325 T
1 T
27326 GTCCCATCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.20
Consensus pattern (32 bp):
TTAGCGAGACCATGGATACATTCAGCCGGGGC
Found at i:31804 original size:14 final size:13
Alignment explanation
Indices: 31711--31805 Score: 76
Period size: 14 Copynumber: 7.4 Consensus size: 13
31701 CCTCCGCAAA
31711 AAAAAAAC-AAAC
1 AAAAAAACAAAAC
31723 AAACAAAACAAAAC
1 AAA-AAAACAAAAC
31737 AAAACAAA-AGAAAC
1 AAAA-AAACA-AAAC
*
31751 AAAAAAA-AAGAAG
1 AAAAAAACAA-AAC
31764 AAAAAAAC-AAAC
1 AAAAAAACAAAAC
* *
31776 AAACAAAC-AGA-
1 AAAAAAACAAAAC
31787 AAAAAAACAACAAC
1 AAAAAAACAA-AAC
31801 AAAAA
1 AAAAA
31806 GGGTCCGGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
11 7 0.10
12 16 0.24
13 22 0.32
14 23 0.34
ACGTcount: A:0.81, C:0.15, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:33301 original size:30 final size:30
Alignment explanation
Indices: 33230--33567 Score: 390
Period size: 30 Copynumber: 11.6 Consensus size: 30
33220 ACATTCCTCA
* *
33230 CTTTTCAAAAGCCCACAAGTCAGTGGCAAC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
***
33260 C--TAGAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
33288 CTTTTCCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
33317 CTTTTCCAAAGCCTACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
33347 CTTTTCCAAAGCCCACAAGTTAGTGGCATC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
***
33377 C--TAGAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
33405 CTTTTCCAAAGCCCACAAGTTAGTGGCA-T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
33434 CTTTTCCAAAGCCCAGAAGTCAATGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
33464 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* *
33494 CTTTTCCAAAACCCACAAGTCAGTGGCAAC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
* * **
33524 C--TTCAAAAGCACACAAGTTGGT-GCAACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGC-ACC
*
33552 C-TTTCAAAAGCCCACA
1 CTTTTCCAAAGCCCACA
33568 CAAGTTGGTG
Statistics
Matches: 263, Mismatches: 37, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
27 2 0.01
28 67 0.25
29 65 0.25
30 129 0.49
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (30 bp):
CTTTTCCAAAGCCCACAAGTCAGTGGCACC
Found at i:33351 original size:59 final size:59
Alignment explanation
Indices: 33230--33526 Score: 409
Period size: 59 Copynumber: 5.1 Consensus size: 59
33220 ACATTCCTCA
* * * ***
33230 CTTTTCAAAAGCCCACAAGTCAGTGGCAAC-CTAGAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACC
*
33288 CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCTACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACC
* * ***
33347 CTTTTCCAAAGCCCACAAGTTAGTGGCATC-CTAGAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACC
* * *
33405 CTTTTCCAAAGCCCACAAGTTAGTGGCATCTTTTCCAAAGCCCAGAAGTCAATGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACC
* * *
33464 CTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAACCCACAAGTCAGTGGCAAC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCACC
33524 CTT
1 CTT
33527 CAAAAGCACA
Statistics
Matches: 211, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
58 81 0.38
59 101 0.48
60 29 0.14
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (59 bp):
CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACC
Found at i:33436 original size:117 final size:117
Alignment explanation
Indices: 33230--33542 Score: 461
Period size: 117 Copynumber: 2.7 Consensus size: 117
33220 ACATTCCTCA
*
33230 CTTTTCAAAAGCCCACAAGTCAGTGGCAACCTAGAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAACCTAGAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * *
33295 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCTACAAGTCAGTGGCACC
66 AAAGCCCACAAGTTAGTGGCATCTTTTCCAAAGCCCACAAGTCAATGGCACC
* *
33347 CTTTTCCAAAGCCCACAAGTTAGTGGCATCCTAGAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAACCTAGAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
33412 AAAGCCCACAAGTTAGTGGCATCTTTTCCAAAGCCCAGAAGTCAATGGCACC
66 AAAGCCCACAAGTTAGTGGCATCTTTTCCAAAGCCCACAAGTCAATGGCACC
* ** *
33464 CTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAA-CCCACAAGTCAGTGGCAACC--T
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAACC---TAGAAAAGCCCACAAGTCAGTGGCACCCTTT
* *
33526 TCAAAAGCACACAAGTT
63 TCCAAAGCCCACAAGTT
33543 GGTGCAACCC
Statistics
Matches: 179, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
117 155 0.87
119 19 0.11
120 5 0.03
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (117 bp):
CTTTTCCAAAGCCCACAAGTCAGTGGCAACCTAGAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
AAAGCCCACAAGTTAGTGGCATCTTTTCCAAAGCCCACAAGTCAATGGCACC
Found at i:33750 original size:98 final size:97
Alignment explanation
Indices: 33594--33882 Score: 347
Period size: 98 Copynumber: 3.0 Consensus size: 97
33584 TCTTCTAAGT
* *
33594 CCAATATCGCTGGCCTTGAATCAGCACATTGACA--C--TTTTAAGTCCAATATCGCTGGCCTTG
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCTTTTTTAAGTCCAATGTCGCTGGCCTTG
* *
33655 AATTAGCATATTGGCACCTTCATCTTTAAAAC
66 AATCAGCACATTGGCACCTTCATCTTTAAAAC
* * * *
33687 CCAAATGTCGTTGGCCTTGAATCAACACATTGGCATTCTTTTTTAAGTCCAATGTCACTGGCCTT
1 CC-AATATCGCTGGCCTTGAATCAGCACATTGGCATTCTTTTTTAAGTCCAATGTCGCTGGCCTT
**
33752 GAATCAGCACATTGGCACCTTCATCTTT-AAGT
65 GAATCAGCACATTGGCACCTTCATCTTTAAAAC
* * * *
33784 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCTTTTTTCACCTTTTAAGTCCAATGTCGCTA
1 CCAATATCGCTGGCCTTGAATCAGCACATT-G-GCATTCTT----TTTTAAGTCCAATGTCGCTG
33849 GCCTTG-ATCAGCACATTGGCACCTTCATCTTTAA
60 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
33883 CATTCCTAAG
Statistics
Matches: 166, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
93 2 0.01
94 28 0.17
96 25 0.15
97 5 0.03
98 55 0.33
101 26 0.16
102 25 0.15
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (97 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCTTTTTTAAGTCCAATGTCGCTGGCCTTG
AATCAGCACATTGGCACCTTCATCTTTAAAAC
Found at i:33800 original size:49 final size:49
Alignment explanation
Indices: 33584--33882 Score: 310
Period size: 49 Copynumber: 6.1 Consensus size: 49
33574 GGTGGCATCT
*
33584 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-A-C-AC-
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
33629 T-TTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
** * * * *
33677 TCTTTAAAACCCAAATGTCGTTGGCCTTGAATCAACACATTGGCA--TTCT
1 TCTTT-AAGTCC-AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
33726 TTTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
33775 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCTTTTTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC---CTTCA
* * *
33827 CCTTTTAAGTCCAATGTCGCTAGCCTTG-ATCAGCACATTGGCACCTTCA
1 TC-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
33876 TCTTTAA
1 TCTTTAA
33883 CATTCCTAAG
Statistics
Matches: 209, Mismatches: 31, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
43 33 0.16
44 3 0.01
45 2 0.01
46 1 0.00
47 30 0.14
48 10 0.05
49 57 0.27
50 4 0.02
51 27 0.13
52 19 0.09
53 23 0.11
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.34
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:34744 original size:19 final size:19
Alignment explanation
Indices: 34720--34770 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
34710 TTTCAATGAT
34720 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
34739 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
34758 TTGTATCGATACA
1 TTGTATCGATACA
34771 ATGTATCGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:34841 original size:13 final size:13
Alignment explanation
Indices: 34823--34847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34813 ATTACTCAAA
34823 TGTATCGATACAT
1 TGTATCGATACAT
34836 TGTATCGATACA
1 TGTATCGATACA
34848 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:34912 original size:52 final size:52
Alignment explanation
Indices: 34856--34984 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
34846 CACTGATCTT
* *
34856 TGTATTGATACATGCAGGCAAATTTGCCCAGATGGATCGATACATTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGGATCGATACACTATGAAA
* *
34908 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGGATCGATACACTATGAAA
*
34960 TGTATCGATACATGTAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
34985 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGGATCGATACACTATGAAA
Done.