Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2083
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: 41000
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Found at i:4513 original size:50 final size:50
Alignment explanation
Indices: 4352--4599 Score: 302
Period size: 50 Copynumber: 4.8 Consensus size: 50
4342 GATAATAACA
* ** *
4352 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGT-CTCGG
* * *
4403 TGCCCATGCCATGTCCCAGACATGGTCTTATA-GGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
*
4452 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
* * *
4502 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--G-TC-T-CGG
*
4557 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4600 TTACCCAAAT
Statistics
Matches: 171, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
48 1 0.01
49 36 0.21
50 60 0.35
51 29 0.17
52 1 0.01
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
Found at i:4529 original size:99 final size:104
Alignment explanation
Indices: 4351--4599 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
4341 TGATAATAAC
**
4351 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
4416 TCCCAGACATGGTCTTATA-GGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
4452 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
4515 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
4557 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4600 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
98 1 0.01
99 39 0.30
100 46 0.35
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:4715 original size:13 final size:13
Alignment explanation
Indices: 4694--4725 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4684 GCTTGGATCA
*
4694 TCATCAAATAAAT
1 TCATAAAATAAAT
4707 TCATAAAATAAAT
1 TCATAAAATAAAT
4720 TCATAA
1 TCATAA
4726 TTGCTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:4971 original size:30 final size:30
Alignment explanation
Indices: 4937--4994 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4927 CCTCGACTCT
**
4937 AACTTTTTTAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
4967 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
4995 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:6143 original size:4 final size:4
Alignment explanation
Indices: 6134--6161 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6124 AGTTTAATGT
6134 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
6162 GATTTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:7879 original size:131 final size:132
Alignment explanation
Indices: 7641--7909 Score: 355
Period size: 131 Copynumber: 2.0 Consensus size: 132
7631 GCTAAGTAAA
* * *
7641 TTTT-ATATGGACTTACTAAGCATTCAATATACTTACTTCAATGTTTCCCTTTTCCTTGTACATT
1 TTTTCATATGAACTTACTAAGCATTCAATATACTTACTCCAATGTTTCCCTTTTCCTTATACATT
* * * *
7705 GTCACTTTGTAGAATATGTTAGACGGATCGTTCAGAAGCTCACAC-TCCTGTTTTCGAATCGGTA
66 GTCACTTTGTAGAATATATCAGACGGATCGTTCAGAAGCTCACACATCCCGTTTTCGAATCGATA
7769 GC
131 GC
* * * * *
7771 TTTTCATATGAACTTACTAGGCATTCAATGTGCTTACTCCAGTGTTT-CCTCTTTCCTTATGCAT
1 TTTTCATATGAACTTACTAAGCATTCAATATACTTACTCCAATGTTTCCCT-TTTCCTTATACAT
* * * *
7835 TGTCACTTTGTGGAATATATCAGGCTGATTGTTCAGAAGCTCACACTATCCCGTTTTCGAATCGA
65 TGTCACTTTGTAGAATATATCAGACGGATCGTTCAGAAGCTCACAC-ATCCCGTTTTCGAATCGA
7900 TAGC
129 TAGC
7904 TTTTCA
1 TTTTCA
7910 AATGTTTTAA
Statistics
Matches: 119, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
130 7 0.06
131 87 0.73
133 25 0.21
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (132 bp):
TTTTCATATGAACTTACTAAGCATTCAATATACTTACTCCAATGTTTCCCTTTTCCTTATACATT
GTCACTTTGTAGAATATATCAGACGGATCGTTCAGAAGCTCACACATCCCGTTTTCGAATCGATA
GC
Found at i:13243 original size:13 final size:15
Alignment explanation
Indices: 13209--13237 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13199 TAAATTGATG
13209 ATAATATATAATAAT
1 ATAATATATAATAAT
13224 ATAATATA-AATAAT
1 ATAATATATAATAAT
13238 GTATATGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATATATAATAAT
Found at i:18749 original size:19 final size:20
Alignment explanation
Indices: 18707--18749 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
18697 AATTTAATTA
*
18707 TTTTTTGCTTATTATTATGT
1 TTTTTTGCTTATTATTATGC
18727 TTTTTTG-TTATTCATT-TGC
1 TTTTTTGCTTATT-ATTATGC
18746 TTTT
1 TTTT
18750 CTATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.12, C:0.07, G:0.09, T:0.72
Consensus pattern (20 bp):
TTTTTTGCTTATTATTATGC
Found at i:20084 original size:22 final size:21
Alignment explanation
Indices: 20057--20143 Score: 99
Period size: 22 Copynumber: 4.2 Consensus size: 21
20047 TAGATTAGAA
*
20057 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTAT-AATT
20079 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTATAATT
*
20100 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTATAATT
* *
20118 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTATAATT
20139 ATTTT
1 -TTTT
20144 ATAATTAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
18 3 0.05
19 14 0.25
20 13 0.23
21 8 0.14
22 19 0.33
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTTGTATGAATATTATAATT
Found at i:20128 original size:19 final size:19
Alignment explanation
Indices: 20081--20137 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
20071 TTTAAATTTT
* *
20081 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
20101 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
20120 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
20138 TATTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:20204 original size:27 final size:26
Alignment explanation
Indices: 20177--20377 Score: 122
Period size: 27 Copynumber: 8.0 Consensus size: 26
20167 TTTGGATTAG
20177 TAATTTTTTGTATGAATATTGTAATA
1 TAATTTTTTGTATGAATATTGTAATA
* *
20203 GTATTATAGTTTTGTATGAATATTG-CA-A
1 -TA--AT-TTTTTGTATGAATATTGTAATA
*
20231 T--TTTTTTGTATGAATATTGTAATT
1 TAATTTTTTGTATGAATATTGTAATA
** *
20255 TTGTAATTTTGTATGAATA-T-T-ATA
1 TAAT-TTTTTGTATGAATATTGTAATA
*
20279 T--TTTTTTGTATGAATGTTGTAATA
1 TAATTTTTTGTATGAATATTGTAATA
* * *
20303 TTATAATTTTGTATGAATATTG-CA-A
1 TAAT-TTTTTGTATGAATATTGTAATA
20328 T--TTTTTTGTATGAATATTGTAATA
1 TAATTTTTTGTATGAATATTGTAATA
** * *
20352 TTGTAATTTTGCATGAATATTGTAAT
1 TAAT-TTTTTGTATGAATATTGTAAT
20378 GTGAGGATAT
Statistics
Matches: 139, Mismatches: 16, Indels: 38
0.72 0.08 0.20
Matches are distributed among these distances:
21 12 0.09
22 34 0.24
23 5 0.04
24 10 0.07
25 3 0.02
26 5 0.04
27 50 0.36
28 1 0.01
29 3 0.02
30 16 0.12
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (26 bp):
TAATTTTTTGTATGAATATTGTAATA
Found at i:20284 original size:49 final size:49
Alignment explanation
Indices: 20180--20373 Score: 284
Period size: 49 Copynumber: 3.9 Consensus size: 49
20170 GGATTAGTAA
*
20180 TTTTTTGTATGAATATTGTAATAGTATTATAGTTTTGTATGAATATTGCAAT
1 TTTTTTGTATGAATATTGT-A-A-TATTATAATTTTGTATGAATATTGCAAT
* *
20232 TTTTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATT--ATAT
1 TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCA-AT
*
20280 TTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAATATTGCAAT
1 TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAAT
* *
20329 TTTTTTGTATGAATATTGTAATATTGTAATTTTGCATGAATATTG
1 TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTG
20374 TAATGTGAGG
Statistics
Matches: 130, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
47 1 0.01
48 43 0.33
49 64 0.49
50 2 0.02
51 1 0.01
52 19 0.15
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (49 bp):
TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAAT
Found at i:20323 original size:19 final size:19
Alignment explanation
Indices: 20299--20356 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 19
20289 TGAATGTTGT
20299 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
**
20318 AATATTGCAATTTTTTTGTATG
1 AATATT---ATAATTTTGTATG
* *
20340 AATATTGTAATATTGTA
1 AATATTATAATTTTGTA
20357 ATTTTGCATG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 13 0.43
22 17 0.57
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:20328 original size:97 final size:100
Alignment explanation
Indices: 20180--20372 Score: 329
Period size: 97 Copynumber: 2.0 Consensus size: 100
20170 GGATTAGTAA
*
20180 TTTTTTGTATGAATATTGTAATAGTATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAA
1 TTTTTTGTATGAATATTGTAATAGTATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAA
* *
20245 TATTGTAATTTTGTAATTTTGTATGAATATTATAT
66 TATTGTAATATTGTAATTTTGCATGAATATTATAT
*
20280 TTTTTTGTATGAATGTTGT-A-A-TATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAA
1 TTTTTTGTATGAATATTGTAATAGTATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAA
20342 TATTGTAATATTGTAATTTTGCATGAATATT
66 TATTGTAATATTGTAATTTTGCATGAATATT
20373 GTAATGTGAG
Statistics
Matches: 89, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
97 69 0.78
98 1 0.01
99 1 0.01
100 18 0.20
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (100 bp):
TTTTTTGTATGAATATTGTAATAGTATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAA
TATTGTAATATTGTAATTTTGCATGAATATTATAT
Found at i:20618 original size:38 final size:38
Alignment explanation
Indices: 20573--20646 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
20563 CATATAAAGT
20573 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
20611 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTT
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTT
20647 GGGTTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:20797 original size:15 final size:15
Alignment explanation
Indices: 20756--20797 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
20746 GTTAACTTAT
*
20756 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
20771 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
20787 TTAAATTTTAT
1 TTAAATTTTAT
20798 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:25234 original size:22 final size:21
Alignment explanation
Indices: 25159--25245 Score: 99
Period size: 20 Copynumber: 4.2 Consensus size: 21
25149 ATTTAATTAT
*
25159 AAAATAATTACAATATTCATAC
1 AAAA-AATTAAAATATTCATAC
* *
25181 --AACATTACAATATTCATA-
1 AAAAAATTAAAATATTCATAC
*
25199 AAAAAATTATAATATTCATAC
1 AAAAAATTAAAATATTCATAC
25220 AAAAAATTTAAAATATTCATAC
1 AAAAAA-TTAAAATATTCATAC
25242 AAAA
1 AAAA
25246 TTCTAATCTA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
19 15 0.26
20 18 0.32
21 6 0.11
22 18 0.32
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAATTAAAATATTCATAC
Found at i:27363 original size:304 final size:299
Alignment explanation
Indices: 26760--27697 Score: 950
Period size: 304 Copynumber: 3.1 Consensus size: 299
26750 TAAATTAATG
* *** *
26760 AAATCTTAAATTTACCACTCAACTAACGTTTCATTTTAATATATTTTATATATTTTTATTTTAAT
1 AAATCTTAAATTTACCACTCAACCAAAACTTCATTTTAATATATTTTATACATTTTTATTTTAAT
* * * * * *
26825 ATGTACAAATTATTATCTCCATTAGTTGTATATCTATATCTATACTTACTATTAATAAAATCGCT
66 ATGCACAATTTATTAT-TTCATCAGTTGTATATCTATA--TATACTTAAT-TTAATAAAATCTCT
* *** * *
26890 AACTAAGTTGGTGTCACGAGTCAACTGGGTAC-CAACTCGATTAGAAAAATTATGAAAATGCCCT
127 AACTGAGTTGGTGTCACGAGTCAAC--CAAACACAACTCGATTAGAAAAATTACGAAAATGTCCT
*
26954 TTCGTAATTAAAGTAAGTCATATTATTCGAAGGCATTTTAGTCTTTTCATTTTAACAAAAACCAA
190 TTCGTAATTAAAGTAA--CATATTATTC-AAGGTATTTTAGTCTTTTCATTTTAACAAAAACCAA
* * * * **
27019 TTAAAATTTGCAT-AGG-GGGATTTGAACCCGCAATAATTGCATTAGTA
252 TAAAAATTTGCATAAGGTGAGAATTGAA-CCTCACCAATTGCATTAGTA
* * *
27066 AAATCTTAAATTTACCACTCAACCAAAACTTCATTTTAATATATTTTATGCATTCTTATTTTACT
1 AAATCTTAAATTTACCACTCAACCAAAACTTCATTTTAATATATTTTATACATTTTTATTTTAAT
* *
27131 ATGCACATTTTATTATATTCATCAGTTGTATATCTATATATACTTAATTTTAATAAAACCTCTAA
66 ATGCACAATTTATTAT-TTCATCAGTTGTATATCTATATATACTTAA-TTTAATAAAATCTCTAA
* *
27196 CTGAGTTGGTGTCATGAGTCAACCAAACACAAACTCGATTAGAAAAATTACAAAAATGTCCTTTC
129 CTGAGTTGGTGTCACGAGTCAACCAAACAC-AACTCGATTAGAAAAATTACGAAAATGTCCTTTC
* * * * *
27261 GTAATTAAAGTAACCGTATTATTCAAGTGTATTTTAGCCATTTCATTCTGACAAAAACCAATAAA
193 GTAATTAAAGTAA-CATATTATTCAAG-GTATTTTAGTCTTTTCATTTTAACAAAAACCAATAAA
*
27326 AATTTGCATAAGGTGAAAATTGAACCTCACCAATTGCATTAGTA
256 AATTTGCATAAGGTGAGAATTGAACCTCACCAATTGCATTAGTA
* * ** * ** *
27370 AAATTTTAAATTTATCACTCAACTGAAATTTCATTTTTGTATATTCTATACATTTTTATTTTAAT
1 AAATCTTAAATTTACCACTCAACCAAAACTTCATTTTAATATATTTTATACATTTTTATTTTAAT
* * * *
27435 ATGCACAATTTACTATTTCCATCAGTTG--TA--TATATGTAC-T-A-TTAATAAAATCTCTGAT
66 ATGCACAATTTATTATTT-CATCAGTTGTATATCTATATATACTTAATTTAATAAAATCTCTAAC
* * * * *
27493 TGAGTTGGTGTCACAAGTCAACCATACATCAACTCGGTTAGAGAAATTACGAAAATGT-CTTCCG
130 TGAGTTGGTGTCACGAGTCAACCAAACA-CAACTCGATTAGAAAAATTACGAAAATGTCCTTTCG
* * * * * *
27557 TGATCAAAGT--CATATTATTCGAGGGTATTTTAATCTTTTTATTTTAACAAAACCCAATAAAAA
194 TAATTAAAGTAACATATTATTC-AAGGTATTTTAGTCTTTTCATTTTAACAAAAACCAATAAAAA
* * * ** * * * *
27620 TATGCATATGGTGCGGGTTGGA-CTCGCTCTAAATGTATTAGTA
258 TTTGCATAAGGTGAGAATTGAACCTCAC-C-AATTGCATTAGTA
* * *
27663 AAACCTTAAATTTATCACTCAATCAAAACTTCATT
1 AAATCTTAAATTTACCACTCAACCAAAACTTCATT
27698 ATTTATTATA
Statistics
Matches: 531, Mismatches: 90, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
291 4 0.01
292 57 0.11
293 42 0.08
295 13 0.02
296 64 0.12
297 1 0.00
298 1 0.00
299 1 0.00
300 8 0.02
302 7 0.01
303 52 0.10
304 184 0.35
305 8 0.02
306 89 0.17
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (299 bp):
AAATCTTAAATTTACCACTCAACCAAAACTTCATTTTAATATATTTTATACATTTTTATTTTAAT
ATGCACAATTTATTATTTCATCAGTTGTATATCTATATATACTTAATTTAATAAAATCTCTAACT
GAGTTGGTGTCACGAGTCAACCAAACACAACTCGATTAGAAAAATTACGAAAATGTCCTTTCGTA
ATTAAAGTAACATATTATTCAAGGTATTTTAGTCTTTTCATTTTAACAAAAACCAATAAAAATTT
GCATAAGGTGAGAATTGAACCTCACCAATTGCATTAGTA
Found at i:27978 original size:26 final size:25
Alignment explanation
Indices: 27942--27990 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
27932 AACTTGACAA
*
27942 TTTTTTTTTAATTTGGCACCTAATT
1 TTTTTTTTTAATTTAGCACCTAATT
*
27967 TTTTTTATTTAATTTAGTACCTAA
1 TTTTTT-TTTAATTTAGCACCTAA
27991 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.59
Consensus pattern (25 bp):
TTTTTTTTTAATTTAGCACCTAATT
Found at i:30787 original size:24 final size:22
Alignment explanation
Indices: 30751--30795 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
30741 AGCAGGGTAG
30751 ATATAAAAATATTGAATATATATA
1 ATATAAAAATATT--ATATATATA
* *
30775 ATATAATATTATTATATATAT
1 ATATAAAAATATTATATATAT
30796 TAAAGTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATAAAAATATTATATATATA
Found at i:30866 original size:14 final size:14
Alignment explanation
Indices: 30849--30882 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
30839 ATATTATAGT
30849 ATATAAAAATAATA
1 ATATAAAAATAATA
*
30863 ATATAATAATAATA
1 ATATAAAAATAATA
30877 A-ATAAA
1 ATATAAA
30883 TAAATGAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATATAAAAATAATA
Found at i:32321 original size:46 final size:45
Alignment explanation
Indices: 32219--32684 Score: 304
Period size: 44 Copynumber: 10.6 Consensus size: 45
32209 TTTAAGTCTA
** * *
32219 CTCCACTGTAATATCAGGGAGATAAGACCTCTG---GCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGA--TCTGAATTCTTCGATCTG
* * *
32263 CTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG-AATTCTTCGATCTG
* * * *
32309 CTCCACTGTAACCTCAGAGAGATAAGACCTG-A---TGCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTG
* * * * ** * *
32350 CTCTACTGTAACTTCAGAGAGATGAGATCCTTTATT-TT-AATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGAT-CTGAATTCTTCGATCTG
* *
32394 CTCCACTGTAACTTCAGGGAGATAGGAT-T--ATATCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTTCGATCTG
* *
32437 CTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG-AATTCTTCGATCTG
* * * * *
32483 TTCCACTGTAATCTCAGGGAGATAAGACCTG-A---TGCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTG
* * * * * *
32524 CTCTACTGTAACTTCAGAGAGATAAGATCCGATATT-TT-AATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGA-ATTCTTCGATCTG
* * * ** *
32568 CTCCACTGTAACTTCAGGGAGATAGGATTTCTA-TCTTTGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTG
* * * * *
32612 CTCCGCTGTAATCTCAAGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG-AATTCTTCGATCTG
* *
32658 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAACCTCAGGGAGATAAGA
32685 CCTGTATTAT
Statistics
Matches: 329, Mismatches: 70, Indels: 44
0.74 0.16 0.10
Matches are distributed among these distances:
40 2 0.01
41 62 0.19
42 10 0.03
43 34 0.10
44 110 0.33
45 3 0.01
46 106 0.32
47 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (45 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTG
Found at i:32416 original size:85 final size:85
Alignment explanation
Indices: 32309--32591 Score: 304
Period size: 87 Copynumber: 3.3 Consensus size: 85
32299 CTTCGGTCTA
* * *
32309 CTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATG
1 CTCCACTGTAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATA
*
32374 AGATCCTTTATTTTAATCCG
66 AGATCCTATATTTTAATCCG
* * * * * ** * *
32394 CTCCACTGTAACTTCAGGGAGATAGGA-TTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
1 CTCCACTGTAACTTCAGGGAGATAAGACCT-GA--TGCGATCTACTCTACTGTAACTTCAGAGAG
** *
32458 ATAAGAT-CTGCA-ATTCTTCGGTCTG
63 ATAAGATCCT--ATATT-TT-AATCCG
*
32483 TTCCACTGTAA-TCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
1 CTCCACTGTAACT-TCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
*
32547 AAGATCCGATATTTTAATCCG
65 AAGATCCTATATTTTAATCCG
32568 CTCCACTGTAACTTCAGGGAGATA
1 CTCCACTGTAACTTCAGGGAGATA
32592 GGATTTCTAT
Statistics
Matches: 155, Mismatches: 31, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
84 1 0.01
85 49 0.32
86 6 0.04
87 67 0.43
88 4 0.03
89 27 0.17
90 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (85 bp):
CTCCACTGTAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATA
AGATCCTATATTTTAATCCG
Found at i:32434 original size:87 final size:87
Alignment explanation
Indices: 32309--32640 Score: 270
Period size: 87 Copynumber: 3.8 Consensus size: 87
32299 CTTCGGTCTA
* * * * * *
32309 CTCCACTGTAACCTCAGAGAGATAAGACCTGA--TGCGATCTACTCTACTGTAACTTCAGAGAGA
1 CTCCACTGTAACTTCAGGGAGATAGGACTTTATCTTCGATCTACTCTACTGTAACTTCAGAGAGA
* *
32372 TGAGATCCTTTATTTTAATCCG
66 TAAGATCCTATATTTTAATCCG
* ** * *
32394 CTCCACTGTAACTTCAGGGAGATAGGA-TTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
1 CTCCACTGTAACTTCAGGGAGATAGGACTT-TATCTTCGATCTACTCTACTGTAACTTCAGAGAG
** *
32458 ATAAGAT-CTGCA-ATTCTTCGGTCTG
65 ATAAGATCCT--ATATT-TT-AATCCG
* * * * *
32483 TTCCACTGTAA-TCTCAGGGAGATAAGACCTGA--TGCGATCTACTCTACTGTAACTTCAGAGAG
1 CTCCACTGTAACT-TCAGGGAGATAGGACTTTATCTTCGATCTACTCTACTGTAACTTCAGAGAG
*
32545 ATAAGATCCGATATTTTAATCCG
65 ATAAGATCCTATATTTTAATCCG
* * * **
32568 CTCCACTGTAACTTCAGGGAGATAGGATTTCTATCTTTGATCTGCTCCGCTGTAA-TCTCA-AGG
1 CTCCACTGTAACTTCAGGGAGATAGGACTT-TATCTTCGATCTACTCTACTGTAACT-TCAGA-G
32631 AGATAAGATC
63 AGATAAGATC
32641 TGAAATTCTT
Statistics
Matches: 190, Mismatches: 40, Indels: 31
0.73 0.15 0.12
Matches are distributed among these distances:
84 1 0.01
85 52 0.27
86 7 0.04
87 69 0.36
88 33 0.17
89 27 0.14
90 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (87 bp):
CTCCACTGTAACTTCAGGGAGATAGGACTTTATCTTCGATCTACTCTACTGTAACTTCAGAGAGA
TAAGATCCTATATTTTAATCCG
Found at i:32473 original size:174 final size:175
Alignment explanation
Indices: 32253--32688 Score: 721
Period size: 174 Copynumber: 2.5 Consensus size: 175
32243 AGACCTCTGG
* * * **
32253 CTTCAATCTGCTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCGGTCTACTCCACTGT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
* * * **
32318 AACCTCAGAGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTT
66 AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCGAT
32383 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TTATAT
131 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTATAT
32427 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
32492 AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCGAT
66 AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCGAT
*
32557 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTCTAT
131 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTATAT
* * * * *
32602 CTTTGATCTGCTCCGCTGTAATCTCAAGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
32667 AATCTCAGGGAGATAAGACCTG
66 AATCTCAGGGAGATAAGACCTG
32689 TATTATGAAC
Statistics
Matches: 245, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
174 158 0.64
175 87 0.36
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (175 bp):
CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCGAT
ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTATAT
Found at i:33858 original size:1 final size:1
Alignment explanation
Indices: 33852--33878 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
33842 TCAAAAGTCC
33852 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
33879 AGGAAGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.