Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014392.1 Corchorus capsularis cultivar CVL-1 contig14413, whole genome shotgun sequence
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: 78542
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:1284 original size:17 final size:17
Alignment explanation
Indices: 1234--1291 Score: 73
Period size: 17 Copynumber: 3.3 Consensus size: 17
1224 CATTCATTTA
1234 ATTTAATATATATTTATT
1 ATTTAA-ATATATTTATT
*
1252 -TTTAACTCATTATTTATT
1 ATTTAAAT-A-TATTTATT
1270 ATTTAAATATATTTATT
1 ATTTAAATATATTTATT
1287 ATTTA
1 ATTTA
1292 TTTATTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 1 0.03
17 19 0.54
18 9 0.26
19 6 0.17
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTAAATATATTTATT
Found at i:1285 original size:21 final size:24
Alignment explanation
Indices: 1260--1309 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
1250 TTTTTAACTC
1260 ATTATTTA-TTATTTA-AATATAT
1 ATTATTTATTTATTTATAATATAT
1282 -TTA-TTATTTATTTATTAATATAT
1 ATTATTTATTTATTTA-TAATATAT
1305 ATTAT
1 ATTAT
1310 ATCTAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
23 7 0.30
24 3 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATTTATTTATTTATAATATAT
Found at i:1870 original size:12 final size:12
Alignment explanation
Indices: 1853--1877 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1843 CGAGATGACT
1853 TCTCTCATTGTA
1 TCTCTCATTGTA
1865 TCTCTCATTGTA
1 TCTCTCATTGTA
1877 T
1 T
1878 TTCACTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TCTCTCATTGTA
Found at i:2453 original size:16 final size:17
Alignment explanation
Indices: 2428--2464 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2418 ATCTGAAATA
2428 CTTT-AGAGCTTTTCTG
1 CTTTCAGAGCTTTTCTG
2444 -TTTCAGAGCTTTTCTG
1 CTTTCAGAGCTTTTCTG
2460 CTTTC
1 CTTTC
2465 TGAATTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (17 bp):
CTTTCAGAGCTTTTCTG
Found at i:10688 original size:3 final size:3
Alignment explanation
Indices: 10682--10716 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
10672 GGAAGCAAGG
10682 AGA AGAA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A
10717 AATAACACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:11944 original size:32 final size:32
Alignment explanation
Indices: 11900--11960 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
11890 AAAAAAGTTT
* *
11900 TAGGCCTTATTTGGTCATTTTGAAGAAAGGTAA
1 TAGGCCTTATTTGATCATTTT-AAAAAAGGTAA
11933 TAGG-CTTATTTGATCATTTTAAAAAAGG
1 TAGGCCTTATTTGATCATTTTAAAAAAGG
11961 GAGAGGGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 7 0.27
32 15 0.58
33 4 0.15
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (32 bp):
TAGGCCTTATTTGATCATTTTAAAAAAGGTAA
Found at i:13252 original size:19 final size:19
Alignment explanation
Indices: 13225--13261 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13215 GCATTTGAAT
*
13225 AAGATTTCAAATCCAACAG
1 AAGAGTTCAAATCCAACAG
13244 AAGAGTTCAAATCCAACA
1 AAGAGTTCAAATCCAACA
13262 AATAGATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.19
Consensus pattern (19 bp):
AAGAGTTCAAATCCAACAG
Found at i:15866 original size:33 final size:33
Alignment explanation
Indices: 15810--15968 Score: 246
Period size: 33 Copynumber: 4.8 Consensus size: 33
15800 TTTGGATTCT
* *
15810 ATTGTTCCCACTAATATTATGCCTCAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
* * *
15843 ATTGCTGCCACTGATGTTGTGCCTCAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
*
15876 ATTGCTCCCACTAATATTGTGCCACAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
*
15909 ATTGCTCCCACTAATAGTGTGCCTCAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
*
15942 ATTGCTTCCACTAATATTGTGCCTCAG
1 ATTGCTCCCACTAATATTGTGCCTCAG
15969 CGAACACACC
Statistics
Matches: 113, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 113 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (33 bp):
ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
Found at i:17658 original size:19 final size:19
Alignment explanation
Indices: 17631--17667 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17621 GCATTTGAAT
*
17631 AAGATTTCAAATCCAACAG
1 AAGAGTTCAAATCCAACAG
17650 AAGAGTTCAAATCCAACA
1 AAGAGTTCAAATCCAACA
17668 AATAGATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.19
Consensus pattern (19 bp):
AAGAGTTCAAATCCAACAG
Found at i:18262 original size:22 final size:22
Alignment explanation
Indices: 18234--18337 Score: 68
Period size: 22 Copynumber: 4.7 Consensus size: 22
18224 ATGACATAGG
* *
18234 AAGGTTATCAAAATTTCATGCAG
1 AAGGTTATCAAAATTTCAT-AAA
*
18257 AA-GTTA-CAAAAATTTTATAAA
1 AAGGTTATC-AAAATTTCATAAA
* *
18278 AAGGTTATCAAAATTTCTTAGA
1 AAGGTTATCAAAATTTCATAAA
** * * **
18300 GGGGTTAACTAAATTTCATACG
1 AAGGTTATCAAAATTTCATAAA
*
18322 AAGGTTATCGAAATTT
1 AAGGTTATCAAAATTT
18338 TATAGTGTGG
Statistics
Matches: 61, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
21 4 0.07
22 54 0.89
23 3 0.05
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AAGGTTATCAAAATTTCATAAA
Found at i:18350 original size:44 final size:44
Alignment explanation
Indices: 18228--18459 Score: 182
Period size: 44 Copynumber: 5.1 Consensus size: 44
18218 ACGAAAATGA
* *
18228 CATAGGAAGGTTATCAAAATTTCAT-GCAGAAGTT-ACAAAAATTT
1 CATAGGAAGGTTATCAAAATTTTATAG-AGAGGTTAAC-AAAATTT
* ** * *
18272 TATAAAAAGGTTATCAAAATTTCT-TAGAGGGGTTAACTAAATTT
1 CATAGGAAGGTTATCAAAATTT-TATAGAGAGGTTAACAAAATTT
* * * *
18316 CATACGAAGGTTATCGAAATTTTATAGTGTGGTTATTAACAAAATTT
1 CATAGGAAGGTTATCAAAATTTTATAGAGAGG---TTAACAAAATTT
** *
18363 CATAGGGAGGGAGGTTATCAAAATTTCCTAGGGAGGTTAACAAAATTT
1 CATA-GGA---AGGTTATCAAAATTTTATAGAGAGGTTAACAAAATTT
* * * * *
18411 CATAGGGAGGTTATGAAAATTTTATGGAGAGGTTATCAAAATTA
1 CATAGGAAGGTTATCAAAATTTTATAGAGAGGTTAACAAAATTT
18455 CATAG
1 CATAG
18460 AGTACTATCA
Statistics
Matches: 149, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
43 1 0.01
44 90 0.60
45 3 0.02
47 17 0.11
48 18 0.12
51 20 0.13
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (44 bp):
CATAGGAAGGTTATCAAAATTTTATAGAGAGGTTAACAAAATTT
Found at i:18387 original size:26 final size:26
Alignment explanation
Indices: 18351--18420 Score: 94
Period size: 22 Copynumber: 2.8 Consensus size: 26
18341 AGTGTGGTTA
18351 TTAACAAAATTTCATAGGGAGGGAGG
1 TTAACAAAATTTCATAGGGAGGGAGG
* *
18377 TTATCAAAATTTCCT----AGGGAGG
1 TTAACAAAATTTCATAGGGAGGGAGG
18399 TTAACAAAATTTCATAGGGAGG
1 TTAACAAAATTTCATAGGGAGG
18421 TTATGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
22 20 0.56
26 16 0.44
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (26 bp):
TTAACAAAATTTCATAGGGAGGGAGG
Found at i:18398 original size:22 final size:21
Alignment explanation
Indices: 18370--18453 Score: 107
Period size: 22 Copynumber: 3.9 Consensus size: 21
18360 TTTCATAGGG
18370 AGGGAGGTTATCAAAATTTCCT
1 AGGGAGGTTATCAAAATTT-CT
*
18392 AGGGAGGTTAACAAAATTTCAT
1 AGGGAGGTTATCAAAATTTC-T
*
18414 AGGGAGGTTATGAAAATTT-T
1 AGGGAGGTTATCAAAATTTCT
18434 ATGGAGAGGTTATCAAAATT
1 A-GG-GAGGTTATCAAAATT
18454 ACATAGAGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.04
21 3 0.05
22 50 0.91
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (21 bp):
AGGGAGGTTATCAAAATTTCT
Found at i:18401 original size:51 final size:48
Alignment explanation
Indices: 18279--18420 Score: 141
Period size: 48 Copynumber: 3.0 Consensus size: 48
18269 TTTTATAAAA
* * *
18279 AGGTTATCAAAATTTCTTAGAGG-GGTTAACTAAATTTCATA-CGA---
1 AGGTTATCAAAATTTCATAG-GGAGGTTAACAAAATTTCATAGGGAGGG
* * * *
18323 AGGTTATCGAAATTTTATAGTGTGGTTATTAACAAAATTTCATAGGGAGGG
1 AGGTTATCAAAATTTCATAGGGAGG---TTAACAAAATTTCATAGGGAGGG
*
18374 AGGTTATCAAAATTTCCTAGGGAGGTTAACAAAATTTCATAGGGAGG
1 AGGTTATCAAAATTTCATAGGGAGGTTAACAAAATTTCATAGGGAGG
18421 TTATGAAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
43 1 0.01
44 19 0.24
47 15 0.19
48 24 0.30
51 20 0.25
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (48 bp):
AGGTTATCAAAATTTCATAGGGAGGTTAACAAAATTTCATAGGGAGGG
Found at i:18526 original size:22 final size:22
Alignment explanation
Indices: 18501--18703 Score: 119
Period size: 22 Copynumber: 9.3 Consensus size: 22
18491 TACATAATCG
* *
18501 AAATTTCATGGTGTGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
*
18523 AAATTTTCATAAT-AGGGTTA-C-
1 AAA-TTTCATAGTGA-GGTTATCA
* * * *
18544 CAATTTTATAGGGAGATTATCA
1 AAATTTCATAGTGAGGTTATCA
* *
18566 AAATTTCACATTGAGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
*** *
18588 AAATTTCATAGTGTCATTGTCA
1 AAATTTCATAGTGAGGTTATCA
* **
18610 AAATTTCACAGTTTGGTTATC-
1 AAATTTCATAGTGAGGTTATCA
* *
18631 AAATTTCATAGAGAGGTTATCG
1 AAATTTCATAGTGAGGTTATCA
* * *
18653 AAATTTCATAATAAGATTATCA
1 AAATTTCATAGTGAGGTTATCA
* * *
18675 AATTTTGACAGT-ATGGTTATCA
1 AAATTTCATAGTGA-GGTTATCA
*
18697 ACATTTC
1 AAATTTC
18704 TATGTTGGAG
Statistics
Matches: 132, Mismatches: 42, Indels: 14
0.70 0.22 0.07
Matches are distributed among these distances:
20 10 0.08
21 22 0.17
22 88 0.67
23 12 0.09
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
AAATTTCATAGTGAGGTTATCA
Found at i:18635 original size:65 final size:65
Alignment explanation
Indices: 18560--18703 Score: 162
Period size: 65 Copynumber: 2.2 Consensus size: 65
18550 TATAGGGAGA
** * ** * *
18560 TTATCAAAATTTCACATTGAGGTTATCAAAATTTCATAGTGTCATTGTCAAAATTTCACAGTTTG
1 TTATC-AAATTTCACAGAGAGGTTATCAAAATTTCATAATAACATTATCAAAATTTCACAGTATG
18625 G
65 G
* * * * *
18626 TTATCAAATTTCATAGAGAGGTTATCGAAATTTCATAATAAGATTATCAAATTTTGACAGTATGG
1 TTATCAAATTTCACAGAGAGGTTATCAAAATTTCATAATAACATTATCAAAATTTCACAGTATGG
18691 TTATCAACATTTC
1 TTATCAA-ATTTC
18704 TATGTTGGAG
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 55 0.85
66 10 0.15
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (65 bp):
TTATCAAATTTCACAGAGAGGTTATCAAAATTTCATAATAACATTATCAAAATTTCACAGTATGG
Found at i:19489 original size:2 final size:2
Alignment explanation
Indices: 19484--19514 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19474 TATATAAGGA
19484 AT AT AT 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
19515 CTAGTCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19723 original size:15 final size:15
Alignment explanation
Indices: 19703--19742 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
19693 GCTCGATCCG
19703 AAACCGAAATGACCC
1 AAACCGAAATGACCC
19718 AAACCGAAATGACCC
1 AAACCGAAATGACCC
* *
19733 GAACCTAAAT
1 AAACCGAAAT
19743 TAACCCGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.47, C:0.30, G:0.12, T:0.10
Consensus pattern (15 bp):
AAACCGAAATGACCC
Found at i:24034 original size:20 final size:21
Alignment explanation
Indices: 23997--24039 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
23987 AACCCGTTAA
*
23997 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
24018 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
24038 TT
1 TT
24040 GACACGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:24097 original size:42 final size:43
Alignment explanation
Indices: 24027--24109 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
24017 CTTAAACGTG
*
24027 TTAATCGTGTCTTGACACGATTACGACACAAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTACGACACAAAACACGATAATC
* *
24070 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATTAC-GACACAAAACACGATAA
24110 GCCAAACACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.03
42 24 0.67
43 11 0.31
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTACGACACAAAACACGATAATC
Found at i:24712 original size:15 final size:15
Alignment explanation
Indices: 24692--24722 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24682 AGTCTAGCTA
24692 CTTGACGAAGGGCTG
1 CTTGACGAAGGGCTG
*
24707 CTTGACGAATGGCTG
1 CTTGACGAAGGGCTG
24722 C
1 C
24723 CAAGTGCCAA
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:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (15 bp):
CTTGACGAAGGGCTG
Found at i:35710 original size:3 final size:3
Alignment explanation
Indices: 35704--35742 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
35694 ATAGTAGTAG
35704 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
35743 AATAATTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:40787 original size:66 final size:66
Alignment explanation
Indices: 40677--40808 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
40667 TCAATGTTGT
*
40677 ATAGTAAAAAACGATTGTCTTATTGCCATTAGAGAAATTGCTAAAGGAGATTCATCTACCTAGCA
1 ATAGTAAAAAACGATTGTCTTATTGCCATTAGAGAAATTACTAAAGGAGATTCATCTACCTAGCA
40742 A
66 A
* *
40743 ATAGTAGAAAGCGATTGTCTTATTGCCATTAGAGAAATTACTAAAGGAGATTCATCTACCTAGCA
1 ATAGTAAAAAACGATTGTCTTATTGCCATTAGAGAAATTACTAAAGGAGATTCATCTACCTAGCA
40808 A
66 A
40809 GGAAGTTGTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (66 bp):
ATAGTAAAAAACGATTGTCTTATTGCCATTAGAGAAATTACTAAAGGAGATTCATCTACCTAGCA
A
Found at i:54187 original size:20 final size:19
Alignment explanation
Indices: 54153--54191 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
54143 AGATTGCGGG
54153 GATTTGTTAGAGAGAGAAA
1 GATTTGTTAGAGAGAGAAA
*
54172 GATTTGATTTGAGAGAGAAA
1 GATTTG-TTAGAGAGAGAAA
54192 AACAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (19 bp):
GATTTGTTAGAGAGAGAAA
Found at i:55434 original size:3 final size:3
Alignment explanation
Indices: 55428--55476 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
55418 CGTCCATTTT
** *
55428 ATC ATC ATC ATC ATC ATC CCC AGC ATC ATC ATC ATC ATC -TCC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT-C ATC
55473 ATC A
1 ATC A
55477 CAATCACAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.31, C:0.39, G:0.02, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:55482 original size:21 final size:21
Alignment explanation
Indices: 55428--55497 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
55418 CGTCCATTTT
*
55428 ATCATCATCATCATCATCCCC
1 ATCATCATCATCATCATCTCC
*
55449 AGCATCATCATCATCATCTCC
1 ATCATCATCATCATCATCTCC
55470 ATCATCA-CAATCA-CAATCTCC
1 ATCATCATC-ATCATC-ATCTCC
55491 ATCATCA
1 ATCATCA
55498 CCGTCCTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 2 0.05
21 42 0.95
ACGTcount: A:0.33, C:0.39, G:0.01, T:0.27
Consensus pattern (21 bp):
ATCATCATCATCATCATCTCC
Found at i:60382 original size:36 final size:36
Alignment explanation
Indices: 60342--60424 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
60332 AACTCCAGCA
*
60342 CCGCCACCTCCACCAGTTCCAGCTAAAGGCCCTGCC
1 CCGCCACCTCCACCAGCTCCAGCTAAAGGCCCTGCC
* *
60378 CCGCCACCTCCACCGGCTCCAGCTAAAGGTCCTGCC
1 CCGCCACCTCCACCAGCTCCAGCTAAAGGCCCTGCC
60414 CCGCCACCTCC
1 CCGCCACCTCC
60425 TCCTCCTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.17, C:0.53, G:0.17, T:0.13
Consensus pattern (36 bp):
CCGCCACCTCCACCAGCTCCAGCTAAAGGCCCTGCC
Found at i:68455 original size:36 final size:35
Alignment explanation
Indices: 68415--68497 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
68405 CTACTTTGCT
68415 ATCTATATTCTCTCTCACTTCACTTTCCACTCTGCA
1 ATCTAT-TTCTCTCTCACTTCACTTTCCACTCTGCA
* * * * *
68451 ATCTAGTTTCTCTGTTACTTCACTTTCCCCTGTGCT
1 ATCTA-TTTCTCTCTCACTTCACTTTCCACTCTGCA
68487 ATCTATGTTCT
1 ATCTAT-TTCT
68498 TCTTAACTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 1 0.03
36 38 0.95
37 1 0.03
ACGTcount: A:0.16, C:0.31, G:0.07, T:0.46
Consensus pattern (35 bp):
ATCTATTTCTCTCTCACTTCACTTTCCACTCTGCA
Found at i:75120 original size:10 final size:10
Alignment explanation
Indices: 75080--75130 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
75070 TTGATGAGAG
75080 GAAAGGAAAA
1 GAAAGGAAAA
75090 GAGAGAGGAAAA
1 GA-A-AGGAAAA
* *
75102 TAAAAGAAAA
1 GAAAGGAAAA
75112 GAAAGGAAAA
1 GAAAGGAAAA
*
75122 GAAAAGAAA
1 GAAAGGAAA
75131 GTTATAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 24 0.71
11 2 0.06
12 8 0.24
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (10 bp):
GAAAGGAAAA
Found at i:75120 original size:20 final size:22
Alignment explanation
Indices: 75080--75130 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
75070 TTGATGAGAG
*
75080 GAAAGGAAAAGAGAGAGGAAAA
1 GAAAAGAAAAGAGAGAGGAAAA
*
75102 TAAAAGAAAAGA-A-AGGAAAA
1 GAAAAGAAAAGAGAGAGGAAAA
75122 GAAAAGAAA
1 GAAAAGAAA
75131 GTTATAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.58
21 1 0.04
22 10 0.38
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (22 bp):
GAAAAGAAAAGAGAGAGGAAAA
Found at i:75121 original size:15 final size:15
Alignment explanation
Indices: 75080--75131 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
75070 TTGATGAGAG
*
75080 GAAAGGAAAAGAGAGAG
1 GAAAGGAAAAGA-A-AA
**
75097 GAAAATAAAAGAAAA
1 GAAAGGAAAAGAAAA
75112 GAAAGGAAAAGAAAA
1 GAAAGGAAAAGAAAA
75127 GAAAG
1 GAAAG
75132 TTATAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 19 0.63
16 1 0.03
17 10 0.33
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (15 bp):
GAAAGGAAAAGAAAA
Found at i:77593 original size:26 final size:26
Alignment explanation
Indices: 77564--77624 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
77554 TTTATTTATT
*
77564 ATATTTATGTAATT-ATAATAGTTGGA
1 ATATGTAT-TAATTCATAATAGTTGGA
*
77590 ATATGTATTTATTCATAATAGTTGGA
1 ATATGTATTAATTCATAATAGTTGGA
77616 ATATGTATT
1 ATATGTATT
77625 TATTTATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.48
Consensus pattern (26 bp):
ATATGTATTAATTCATAATAGTTGGA
Found at i:77625 original size:26 final size:26
Alignment explanation
Indices: 77578--77628 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
77568 TTATGTAATT
77578 ATAATAGTTGGAATATGTATTTATTC
1 ATAATAGTTGGAATATGTATTTATTC
77604 ATAATAGTTGGAATATGTATTTATT
1 ATAATAGTTGGAATATGTATTTATT
77629 TATACATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (26 bp):
ATAATAGTTGGAATATGTATTTATTC
Found at i:77629 original size:30 final size:29
Alignment explanation
Indices: 77565--77631 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 29
77555 TTATTTATTA
*
77565 TATTTATGTAATTATAATAGTTGGAATATG
1 TATTTAT-TTATTATAATAGTTGGAATATG
*
77595 TATTTA--T-TCATAATAGTTGGAATATG
1 TATTTATTTATTATAATAGTTGGAATATG
77621 TATTTATTTAT
1 TATTTATTTAT
77632 ACATGTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
26 24 0.75
28 1 0.03
29 1 0.03
30 6 0.19
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.51
Consensus pattern (29 bp):
TATTTATTTATTATAATAGTTGGAATATG
Done.