Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1818
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: 81306
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:223 original size:22 final size:22
Alignment explanation
Indices: 149--223 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
139 TGTGATATAC
*
149 ACATACT-TTATAGTAATATAT
1 ACATACTATTATAGTAATATGT
* *
170 ACATACTATT-T-GTGATGTGT
1 ACATACTATTATAGTAATATGT
* *
190 ACATTC-AGTTATAGTCATATGT
1 ACATACTA-TTATAGTAATATGT
212 ACATACTATTAT
1 ACATACTATTAT
224 TGTGATAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
19 1 0.02
20 13 0.31
21 9 0.21
22 18 0.43
23 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (22 bp):
ACATACTATTATAGTAATATGT
Found at i:9524 original size:22 final size:21
Alignment explanation
Indices: 9481--9531 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
9471 CGGAAACAAA
9481 AAGGGGGAAAGATATTTTATT
1 AAGGGGGAAAGATATTTTATT
*
9502 AAGGGGAGAAA-ATTTTTTAATT
1 AAGGGG-GAAAGATATTTT-ATT
9524 AAGGGGGA
1 AAGGGGGA
9532 GTTATAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.29
Consensus pattern (21 bp):
AAGGGGGAAAGATATTTTATT
Found at i:10203 original size:32 final size:33
Alignment explanation
Indices: 10143--10204 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
10133 GACCTAGAAG
*
10143 TATCGATACATATTGCTTTGTATCGATATACTA
1 TATCGATACATATTGCTTGGTATCGATATACTA
10176 TATCGATACATGA-T-CTTGGTATCGATATA
1 TATCGATACAT-ATTGCTTGGTATCGATATA
10205 GAACAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 12 0.44
34 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (33 bp):
TATCGATACATATTGCTTGGTATCGATATACTA
Found at i:10289 original size:13 final size:13
Alignment explanation
Indices: 10271--10301 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
10261 CGATACATGG
*
10271 TACATTGTATTGA
1 TACATTGTATCGA
10284 TACATTGTATCGA
1 TACATTGTATCGA
10297 TACAT
1 TACAT
10302 AGTGAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:13181 original size:21 final size:21
Alignment explanation
Indices: 13151--13207 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
13141 TTATATAAAA
13151 TTTAA-ATTTAATTTTTAATC
1 TTTAATATTTAATTTTTAATC
*
13171 TTTAATATTT-ATAATTTAATC
1 TTTAATATTTAAT-TTTTAATC
**
13192 TTTTTTA-TTAATTTTT
1 TTTAATATTTAATTTTT
13208 GTGGTATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTAATATTTAATTTTTAATC
Found at i:14956 original size:153 final size:155
Alignment explanation
Indices: 14652--14982 Score: 404
Period size: 153 Copynumber: 2.1 Consensus size: 155
14642 AGGTATATTC
** * *
14652 TAGGGGCATTTTTGTAATTTTTCAAAATCAACTCCTAGGTTGTCACCAGGTTCGCTTTTATGCCG
1 TAGGGGCATTTTCATAATTTTTTAAAACCAACTCCTAGGTTGTCACCAGGTTCGCTTTTATGCCG
* * * *
14717 AAGGTGGGTATTTAGAATAGGTTTATCCTGTCTATAATCCTTTTCATGTCCTTTAGGAGTATCAG
66 AAGGTGGGTATTTAGAATAGATTTATCCTATCTATAATCATTTTCAAGTCCTTTAGGAGTATCAG
* *
14782 ACACTTCTACATTAAAGGTATCCCT
131 ACACTTCTACATGAAAGGTATCCCG
* *
14807 TA-GGGCA-TTTCATAATTTTTTAGAACCAAGTCCTAGGTTGTCACCAGGTAT-GCTTTTATGCC
1 TAGGGGCATTTTCATAATTTTTTAAAACCAACTCCTAGGTTGTCACCAGGT-TCGCTTTTATGCC
* * * *
14869 GAAGGTGGGTATTTAGGATA-ATTTCATCCTATCTATAATCATTTTTAAGTCCTTTAGGGGTATT
65 GAAGGTGGGTATTTAGAATAGATTT-ATCCTATCTATAATCATTTTCAAGTCCTTTAGGAGTATC
* ** *
14933 GGGTATTTCTA-AGTCGAAA-GTATCCCG
129 AGACACTTCTACA-T-GAAAGGTATCCCG
14960 TAGGGGCATTTTCATAATTTTTT
1 TAGGGGCATTTTCATAATTTTTT
14983 TTTAGGATCG
Statistics
Matches: 150, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
152 4 0.03
153 116 0.77
154 14 0.09
155 16 0.11
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (155 bp):
TAGGGGCATTTTCATAATTTTTTAAAACCAACTCCTAGGTTGTCACCAGGTTCGCTTTTATGCCG
AAGGTGGGTATTTAGAATAGATTTATCCTATCTATAATCATTTTCAAGTCCTTTAGGAGTATCAG
ACACTTCTACATGAAAGGTATCCCG
Found at i:26771 original size:95 final size:95
Alignment explanation
Indices: 26564--26808 Score: 319
Period size: 95 Copynumber: 2.6 Consensus size: 95
26554 TTTTTTGTTG
* * *
26564 AAAAATGAGGTTGGAGTATCCCCTCGGAGGAATGGAGTTAGAGTGTTCCCGATAATGATATTTTA
1 AAAAATGAGGTTGGAGTATCCCCTCGGAAGAATGGAGTTGGAGTGTCCCCGATAATGATATTTTA
* *
26629 GGCAAAAATAGGAAGTATCTTGACAAATTT
66 GGAAAAAATAGGAAGTATCTTAACAAATTT
* * * * * * *
26659 AAAAACGAGATTAGAGTATCCCCTTGGAAAAATGAAGTTGGAATGTCCCCGATAATGATATTTTA
1 AAAAATGAGGTTGGAGTATCCCCTCGGAAGAATGGAGTTGGAGTGTCCCCGATAATGATATTTTA
* *
26724 GGAAAAAATAGGAAGTATCTTAATAAGTTT
66 GGAAAAAATAGGAAGTATCTTAACAAATTT
* * * * *
26754 AAAAATGGGGTTGGAGTATTCTCTCGGAAGAATGGGGTTGGAGTGTCGCCGATAA
1 AAAAATGAGGTTGGAGTATCCCCTCGGAAGAATGGAGTTGGAGTGTCCCCGATAA
26809 ATAAAAGTTT
Statistics
Matches: 124, Mismatches: 26, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
95 124 1.00
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (95 bp):
AAAAATGAGGTTGGAGTATCCCCTCGGAAGAATGGAGTTGGAGTGTCCCCGATAATGATATTTTA
GGAAAAAATAGGAAGTATCTTAACAAATTT
Found at i:29047 original size:20 final size:20
Alignment explanation
Indices: 28980--29057 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
28970 AAAAACCCAG
* *
28980 ATGTATCGATACAATGATAA
1 ATGTATCGATACATTTATAA
*
29000 ATGTATCGATATA-TTATGAA
1 ATGTATCGATACATTTAT-AA
*
29020 GCATGTATCGATACATTTATTA
1 --ATGTATCGATACATTTATAA
*
29042 ATGTATCAATACATTT
1 ATGTATCGATACATTT
29058 CCTTGGCAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.06
20 29 0.59
22 13 0.27
23 4 0.08
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTATAA
Found at i:30510 original size:20 final size:20
Alignment explanation
Indices: 30462--30520 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
30452 TATAATGAGA
*
30462 AATGTATCGATACAATTGCAAG
1 AATGTATCGATAC-ATT-TAAG
* *
30484 CATGTATCGATACATTTAAT
1 AATGTATCGATACATTTAAG
*
30504 AATGTATCAATACATTT
1 AATGTATCGATACATTT
30521 CCTTGGTAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 17 0.53
21 3 0.09
22 12 0.38
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTTAAG
Found at i:30582 original size:19 final size:20
Alignment explanation
Indices: 30558--30611 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
30548 ATTGATACAT
30558 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGTA
** *
30577 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-AAACTGTA
30598 TGTATCGATACAAA
1 TGTATCGATACAAA
30612 TTGTAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAAACTGTA
Found at i:31779 original size:3 final size:3
Alignment explanation
Indices: 31771--31811 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
31761 TTCTATAGAT
* *
31771 GAA GAA GAA GAA AAA GAA GAA AAA GAA GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
31812 AAATCATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:32334 original size:29 final size:26
Alignment explanation
Indices: 32296--32358 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
32286 TTGAACTTAA
*
32296 AAATATTTAAATACTAAATAAAAGTAAT
1 AAATAATTAAAT--TAAATAAAAGTAAT
* *
32324 ATAATAATTAAATTTAATAAAATTAAT
1 A-AATAATTAAATTAAATAAAAGTAAT
32351 AAATAATT
1 AAATAATT
32359 TTAAAAAGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 7 0.23
27 13 0.42
28 1 0.03
29 10 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
AAATAATTAAATTAAATAAAAGTAAT
Found at i:33252 original size:28 final size:27
Alignment explanation
Indices: 33203--33255 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
33193 AAAATCTTAT
*
33203 GTAAAAATATTTAAAAACATTCTATGA
1 GTAAAAATATTTAAAAAAATTCTATGA
33230 GTAAAAA-ATTTAATTAAAAATTCTAT
1 GTAAAAATATTTAA--AAAAATTCTAT
33256 ACATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 7 0.30
28 10 0.43
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (27 bp):
GTAAAAATATTTAAAAAAATTCTATGA
Found at i:33546 original size:19 final size:20
Alignment explanation
Indices: 33496--33546 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
33486 TGATTTCACT
*
33496 AAAGTATCAATACTATGAAG
1 AAAGTATCGATACTATGAAG
* * *
33516 AAAATATTGATACTTTG-AG
1 AAAGTATCGATACTATGAAG
33535 AAAGTATCGATA
1 AAAGTATCGATA
33547 TCTCAATACA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (20 bp):
AAAGTATCGATACTATGAAG
Found at i:35346 original size:20 final size:20
Alignment explanation
Indices: 35323--35395 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
35313 ACAATTCAAA
35323 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
35343 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
35364 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
35384 GTATCGATACAT
1 GTATCGATACAT
35396 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:35374 original size:41 final size:42
Alignment explanation
Indices: 35323--35417 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
35313 ACAATTCAAA
*
35323 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
35364 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
35406 GTATCGATACAT
1 GTATCGATACAT
35418 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:35474 original size:13 final size:13
Alignment explanation
Indices: 35456--35481 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35446 TACAGCAAGT
35456 ATGTATCGATACA
1 ATGTATCGATACA
35469 ATGTATCGATACA
1 ATGTATCGATACA
35482 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:39563 original size:15 final size:15
Alignment explanation
Indices: 39543--39573 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39533 TAAAAATGTC
*
39543 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
39558 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
39573 C
1 C
39574 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:41656 original size:20 final size:20
Alignment explanation
Indices: 41628--41666 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41618 CATCTGGAAA
41628 TTCTATGTATCGATACATTT
1 TTCTATGTATCGATACATTT
*
41648 TTCTTTGTATCGATACATT
1 TTCTATGTATCGATACATT
41667 GTATCGATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.51
Consensus pattern (20 bp):
TTCTATGTATCGATACATTT
Found at i:41670 original size:13 final size:13
Alignment explanation
Indices: 41652--41690 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
41642 ACATTTTTCT
41652 TTGTATCGATACA
1 TTGTATCGATACA
41665 TTGTATCGATACA
1 TTGTATCGATACA
*
41678 CTGTATCGATACA
1 TTGTATCGATACA
41691 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:44156 original size:20 final size:20
Alignment explanation
Indices: 44133--44205 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
44123 ACAATTCAAA
44133 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
44153 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
44174 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
44194 GTATCGATACAT
1 GTATCGATACAT
44206 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:44184 original size:41 final size:42
Alignment explanation
Indices: 44133--44227 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
44123 ACAATTCAAA
*
44133 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
44174 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
44216 GTATCGATACAT
1 GTATCGATACAT
44228 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:44284 original size:13 final size:13
Alignment explanation
Indices: 44266--44291 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44256 TACAGCAAGT
44266 ATGTATCGATACA
1 ATGTATCGATACA
44279 ATGTATCGATACA
1 ATGTATCGATACA
44292 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:45844 original size:13 final size:13
Alignment explanation
Indices: 45826--45850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45816 CATTATGCTT
45826 TGTATCGATACAA
1 TGTATCGATACAA
45839 TGTATCGATACA
1 TGTATCGATACA
45851 TGTTCATTGT
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:45847 original size:33 final size:32
Alignment explanation
Indices: 45805--45869 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
45795 ACACACCCAG
*
45805 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
45838 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
45870 TTGATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:45863 original size:19 final size:19
Alignment explanation
Indices: 45839--45892 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
45829 ATCGATACAA
* *
45839 TGTATCGATACATGTTCAT
1 TGTATCGATACATGATAAT
45858 TGTATCGATACATTGATAAT
1 TGTATCGATACA-TGATAAT
*
45878 TATATCGATACATGA
1 TGTATCGATACATGA
45893 AACTGGTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGATAAT
Found at i:49904 original size:13 final size:13
Alignment explanation
Indices: 49886--49912 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49876 TATAATGAAC
49886 ATGTATCGATACA
1 ATGTATCGATACA
49899 ATGTATCGATACA
1 ATGTATCGATACA
49912 A
1 A
49913 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:54218 original size:13 final size:13
Alignment explanation
Indices: 54200--54224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54190 AAATTCGTAA
54200 TGTATCGATACAT
1 TGTATCGATACAT
54213 TGTATCGATACA
1 TGTATCGATACA
54225 ATATGCCATG
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:54319 original size:19 final size:19
Alignment explanation
Indices: 54274--54329 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
54264 CTGCCAGTTT
**
54274 CATGTATTGATACAATTGTG
1 CATGTATTGATACAA-TGAA
54294 CATGTATTGATACAATGAA
1 CATGTATTGATACAATGAA
* * *
54313 TATGTATCGATATAATG
1 CATGTATTGATACAATG
54330 TATCAATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (19 bp):
CATGTATTGATACAATGAA
Found at i:57156 original size:20 final size:21
Alignment explanation
Indices: 57123--57162 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
57113 AATGAATCTG
*
57123 AAAAAAATACTCAAT-TAAAA
1 AAAAAAACACTCAATGTAAAA
*
57143 AAAAAAACATTCAATGTAAA
1 AAAAAAACACTCAATGTAAA
57163 TTATAAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.68, C:0.10, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAAAAACACTCAATGTAAAA
Found at i:63159 original size:21 final size:21
Alignment explanation
Indices: 63129--63181 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
63119 TTTTACAATT
63129 TGTATTGATACAAATA-GTAAA
1 TGTATTGATAC-AATACGTAAA
*
63150 TGTATCGATAC-ATACGTAAA
1 TGTATTGATACAATACGTAAA
63170 TGTATTGATACA
1 TGTATTGATACA
63182 TGCCTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 15 0.54
21 10 0.36
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (21 bp):
TGTATTGATACAATACGTAAA
Found at i:63189 original size:20 final size:20
Alignment explanation
Indices: 63146--63194 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
63136 ATACAAATAG
*
63146 TAAATGTATCGATACATACG
1 TAAATGTATCGATACATACC
* *
63166 TAAATGTATTGATACATGCC
1 TAAATGTATCGATACATACC
63186 TAAAATGTA
1 T-AAATGTA
63195 CAATACAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (20 bp):
TAAATGTATCGATACATACC
Found at i:65639 original size:79 final size:79
Alignment explanation
Indices: 65538--66113 Score: 572
Period size: 79 Copynumber: 7.3 Consensus size: 79
65528 TTTTTTTGTC
* * ** *
65538 ATTTCCAAAATATGATTTTTTCACCATCAAGGATACTCCAACCCCGTTATTTCT-GAGGAAATAC
1 ATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTT-TAGAGGAGATAC
* *
65602 TCTAAACTCATTTTT
65 TCTAACCCCATTTTT
* * * *
65617 ATTTTCAAAATATCGATTTTTCACCATCGGGGATACTCCAACCCTGTTATTTCTAAAGG-GATAC
1 ATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTT-TAGAGGAGATAC
* * * *
65681 TCCAACCTCGTTTTC
65 TCTAACCCCATTTTT
* * ** * * * * *
65696 ATTTCCAAAATATCAATTTTTTACTATCGATGATACTCTAACCTCATTATTTTTGAGGGGATACT
1 ATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTAGAGGAGATACT
* *
65761 CTAACCTCGTTTTT
66 CTAACCCCATTTTT
* * * * * *
65775 ATTTCTAAAATATCAATTTTTCACTATCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACT
1 ATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTAGAGGAGATACT
* *
65840 CCAACCCCGTTTTT
66 CTAACCCCATTTTT
* * *
65854 ATTTCCAAAATATCAATTTTTCATCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACT
1 ATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTAGAGGAGATACT
65919 -TCAACCCCATTTTT
66 CT-AACCCCATTTTT
* * * * * *
65933 ATTTCTAAAAGATCGATTTTTCACCATTGGGGATACTCCAACTCCGTTATTTCTA-A-CAGGATA
1 ATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTT-TAGAGGA-GATA
65996 CTCTAACCCCGA-TTTT
64 CTCTAACCCC-ATTTTT
* ** ** *
66012 ATTT-CAAAATATCAGTTTTTCACCATTAGGGATACTCCAACCTTGTTATTTTCGAGGAGATACT
1 ATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTAGAGGAGATACT
*
66076 CCAACCCCATTTTT
66 CTAACCCCATTTTT
* *
66090 ATCTCCAAAATATTAAATTTTTCA
1 ATTTCCAAAATA-TCAATTTTTCA
66114 TCATGGAATA
Statistics
Matches: 418, Mismatches: 67, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
77 2 0.00
78 65 0.16
79 336 0.80
80 15 0.04
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (79 bp):
ATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTAGAGGAGATACT
CTAACCCCATTTTT
Found at i:65825 original size:158 final size:158
Alignment explanation
Indices: 65536--66113 Score: 661
Period size: 158 Copynumber: 3.7 Consensus size: 158
65526 GATTTTTTTG
* * * * *
65536 TCATTTCCAAAATATGATTTTTTCACCATCAAGGATACTCCAACCCCGTTA-TTTCTGAGGAAAT
1 TCATTTCCAAAATATCAATTTTTCACCATCGAGGATACTCCAACCTCGTTATTTTC-GAGGAGAT
* * * *
65600 ACTCTAAACTCATTTTTATTT-TCAAAATATCGATTTTTCACCATCGGGGATACTCCAACCCTGT
65 ACTCTAACCCCATTTTTATTTCT-AAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGT
*
65664 TATTTCTAAAGGGATACTCCAACCTCGTTT
129 TATTTCTAAAGGGATACTCCAACCCCGTTT
* * * * * * *
65694 TCATTTCCAAAATATCAATTTTTTACTATCGATGATACTCTAACCTCATTATTTTTGAGGGGATA
1 TCATTTCCAAAATATCAATTTTTCACCATCGAGGATACTCCAACCTCGTTATTTTCGAGGAGATA
* * * * *
65759 CTCTAACCTCGTTTTTATTTCTAAAATATCAATTTTTCACTATCGAGGATACTCCAACCCCATTA
66 CTCTAACCCCATTTTTATTTCTAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTA
* *
65824 TTT-TCGAGGGGATACTCCAACCCCGTTT
131 TTTCT-AAAGGGATACTCCAACCCCGTTT
* * *
65852 TTATTTCCAAAATATCAATTTTTCATCATCGGGGATACTCCAACC-CTGTTATTTTCGAGGAGAT
1 TCATTTCCAAAATATCAATTTTTCACCATCGAGGATACTCCAACCTC-GTTATTTTCGAGGAGAT
* * * *
65916 ACT-TCAACCCCATTTTTATTTCTAAAAGATCGATTTTTCACCATTGGGGATACTCCAACTCCGT
65 ACTCT-AACCCCATTTTTATTTCTAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGT
*
65980 TATTTCTAACA-GGATACTCTAACCCCGATTT
129 TATTTCTAA-AGGGATACTCCAACCCCG-TTT
* * *
66011 T-ATTT-CAAAATATCAGTTTTTCACCAT-TAGGGATACTCCAACCTTGTTATTTTCGAGGAGAT
1 TCATTTCCAAAATATCAATTTTTCACCATCGA-GGATACTCCAACCTCGTTATTTTCGAGGAGAT
* * * *
66073 ACTCCAACCCCATTTTTATCTCCAAAATATTAAATTTTTCA
65 ACTCTAACCCCATTTTTATTTCTAAAATA-TCAATTTTTCA
66114 TCATGGAATA
Statistics
Matches: 353, Mismatches: 55, Indels: 24
0.82 0.13 0.06
Matches are distributed among these distances:
157 77 0.22
158 267 0.76
159 9 0.03
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (158 bp):
TCATTTCCAAAATATCAATTTTTCACCATCGAGGATACTCCAACCTCGTTATTTTCGAGGAGATA
CTCTAACCCCATTTTTATTTCTAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTA
TTTCTAAAGGGATACTCCAACCCCGTTT
Found at i:65970 original size:237 final size:236
Alignment explanation
Indices: 65538--66117 Score: 698
Period size: 237 Copynumber: 2.4 Consensus size: 236
65528 TTTTTTTGTC
* * *
65538 ATTTCCAAAATATGATTTTTTCACCATCAAGGATACTCCAACCCCGTTA-TTTCTGAGGAAATAC
1 ATTT-CAAAATATCAATTTTTCACCATCAAGGATACTCCAACCCCGTTATTTTC-GAGGAGATAC
* * * * * *
65602 TCTAAACTCATTTTTATTTTCAAAATATCGATTTTTCACCATCGGGGATACTCCAACCCTGTTAT
64 TCCAACCCCATTTTTATTTCCAAAATATCAATTTTTCATCATCGGGGATACTCCAACCCTGTTAT
* * * * * *
65667 TTCTAAAGGGATACTCCAACCTCGTTTTCATTTCCAAAATATCAATTTTTTACTATCGATGATAC
129 TTCTAAAGGGATACTCCAACCCCATTTTCATTTCCAAAAGATCAATTTTTCACCATCGAGGATAC
* * * ** * *
65732 TCTAAC-CTCATTATTTTTGAGGGGATACTCTAACCTCGTTTTT
194 TCCAACTC-CATTATTTCTAACAGGATACTCTAACCCCGATTTT
* * * *
65775 ATTTCTAAAATATCAATTTTTCACTATCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACT
1 ATTTC-AAAATATCAATTTTTCACCATCAAGGATACTCCAACCCCGTTATTTTCGAGGAGATACT
*
65840 CCAACCCCGTTTTTATTTCCAAAATATCAATTTTTCATCATCGGGGATACTCCAACCCTGTTATT
65 CCAACCCCATTTTTATTTCCAAAATATCAATTTTTCATCATCGGGGATACTCCAACCCTGTTATT
** * * * * * *
65905 T-TCGAGGAGATACTTCAACCCCATTTTTATTTCTAAAAGATCGATTTTTCACCATTGGGGATAC
130 TCTAAAGG-GATACTCCAACCCCATTTTCATTTCCAAAAGATCAATTTTTCACCATCGAGGATAC
*
65969 TCCAACTCCGTTATTTCTAACAGGATACTCTAACCCCGATTTT
194 TCCAACTCCATTATTTCTAACAGGATACTCTAACCCCGATTTT
* * * **
66012 ATTTCAAAATATCAGTTTTTCACCATTAGGGATACTCCAACCTTGTTATTTTCGAGGAGATACTC
1 ATTTCAAAATATCAATTTTTCACCATCAAGGATACTCCAACCCCGTTATTTTCGAGGAGATACTC
* *
66077 CAACCCCATTTTTATCTCCAAAATATTAAATTTTTCATCAT
66 CAACCCCATTTTTATTTCCAAAATA-TCAATTTTTCATCAT
66118 GGAATATACT
Statistics
Matches: 290, Mismatches: 48, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
236 79 0.27
237 206 0.71
238 5 0.02
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (236 bp):
ATTTCAAAATATCAATTTTTCACCATCAAGGATACTCCAACCCCGTTATTTTCGAGGAGATACTC
CAACCCCATTTTTATTTCCAAAATATCAATTTTTCATCATCGGGGATACTCCAACCCTGTTATTT
CTAAAGGGATACTCCAACCCCATTTTCATTTCCAAAAGATCAATTTTTCACCATCGAGGATACTC
CAACTCCATTATTTCTAACAGGATACTCTAACCCCGATTTT
Found at i:71726 original size:2 final size:2
Alignment explanation
Indices: 71714--71743 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
71704 TTTACCATTC
71714 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71744 AAATATAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:72200 original size:3 final size:3
Alignment explanation
Indices: 72192--72230 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
72182 TTTCAACTAA
72192 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
72231 TTTGGTAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:73386 original size:8 final size:8
Alignment explanation
Indices: 73373--73438 Score: 87
Period size: 8 Copynumber: 8.2 Consensus size: 8
73363 TTTTGAGCAG
73373 ATATATAT
1 ATATATAT
73381 ATATATAT
1 ATATATAT
*
73389 ATATATGT
1 ATATATAT
73397 ATATATAT
1 ATATATAT
*
73405 GTATATAT
1 ATATATAT
*
73413 GTATATAT
1 ATATATAT
*
73421 ATGTATAT
1 ATATATAT
*
73429 ATATGTAT
1 ATATATAT
73437 AT
1 AT
73439 TTCTTTCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 51 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (8 bp):
ATATATAT
Found at i:73388 original size:10 final size:10
Alignment explanation
Indices: 73373--73438 Score: 87
Period size: 10 Copynumber: 6.6 Consensus size: 10
73363 TTTTGAGCAG
73373 ATATATATAT
1 ATATATATAT
73383 ATATATATAT
1 ATATATATAT
*
73393 ATGTATATAT
1 ATATATATAT
*
73403 ATGTATATAT
1 ATATATATAT
*
73413 GTATATATAT
1 ATATATATAT
*
73423 GTATATATAT
1 ATATATATAT
*
73433 GTATAT
1 ATATAT
73439 TTCTTTCAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 53 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:73399 original size:18 final size:18
Alignment explanation
Indices: 73373--73438 Score: 96
Period size: 18 Copynumber: 3.6 Consensus size: 18
73363 TTTTGAGCAG
*
73373 ATATATATATATATATAT
1 ATATGTATATATATATAT
*
73391 ATATGTATATATATGTAT
1 ATATGTATATATATATAT
73409 ATATGTATATATATGTATAT
1 ATATGTATATATA--TATAT
73429 ATATGTATAT
1 ATATGTATAT
73439 TTCTTTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 29 0.67
20 14 0.33
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
ATATGTATATATATATAT
Found at i:73763 original size:21 final size:22
Alignment explanation
Indices: 73726--73773 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
73716 AATGTTATAA
73726 ATATTAAAATTTGAATTTAAAG
1 ATATTAAAATTTGAATTTAAAG
*
73748 ATATT-AAATATT-AATTTAAAT
1 ATATTAAAAT-TTGAATTTAAAG
73769 ATATT
1 ATATT
73774 TATATGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATTAAAATTTGAATTTAAAG
Found at i:74807 original size:35 final size:35
Alignment explanation
Indices: 74761--74832 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
74751 ATTTTCAAAT
* *
74761 CATTCTAACCTGGCCATGCATAGGTCTTATTAAAC
1 CATTCTAACCTGACCATGCATAGGTCTTACTAAAC
*
74796 CATTCTAACCTGACCATGTATAGGTCTTACTAAAC
1 CATTCTAACCTGACCATGCATAGGTCTTACTAAAC
74831 CA
1 CA
74833 AAGCTCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (35 bp):
CATTCTAACCTGACCATGCATAGGTCTTACTAAAC
Found at i:74870 original size:14 final size:14
Alignment explanation
Indices: 74848--74877 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
74838 CAAATTAATA
74848 ATGCACTAATTATT
1 ATGCACTAATTATT
*
74862 ATGCGCTAATTATT
1 ATGCACTAATTATT
74876 AT
1 AT
74878 TATGGATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (14 bp):
ATGCACTAATTATT
Found at i:76955 original size:55 final size:57
Alignment explanation
Indices: 76882--77035 Score: 231
Period size: 58 Copynumber: 2.7 Consensus size: 57
76872 ATGTTTAAGG
* * *
76882 TAACTAGATCTAAGTTAGGTTTTAACTAGTGAA-AAAAGGGTCTTATTAACTGCATA
1 TAACTAGATCTAAGTTAGGTTTTAACTAGTGAACAAAAGGGTCTTATTAACAGAAGA
* *
76938 T-ACTAGATCTAAATTAGGTTTTAACTAATGAACAAAAGGGTCTTATTAACAGAAGA
1 TAACTAGATCTAAGTTAGGTTTTAACTAGTGAACAAAAGGGTCTTATTAACAGAAGA
*
76994 TAAGCTAGATCTAAGTTAGGGTTTAACTAGTGAACAAAAGGG
1 TAA-CTAGATCTAAGTTAGGTTTTAACTAGTGAACAAAAGGG
77036 AGCATGAAGC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
55 29 0.33
56 22 0.25
57 1 0.01
58 35 0.40
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (57 bp):
TAACTAGATCTAAGTTAGGTTTTAACTAGTGAACAAAAGGGTCTTATTAACAGAAGA
Done.