Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold745
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: 74167
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:1358 original size:2 final size:2
Alignment explanation
Indices: 1351--1392 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1341 AGATTTTCAA
*
1351 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1392 A
1 A
1393 AATAAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4835 original size:20 final size:20
Alignment explanation
Indices: 4810--4864 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
4800 AAAATGCTTG
4810 AATGTATCGATACATTGAGA
1 AATGTATCGATACATTGAGA
*
4830 AATGTATCGATAAATTGAGA
1 AATGTATCGATACATTGAGA
4850 AATGTATCGATACAT
1 AATGTATCGATACAT
4865 CTGGATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGAGA
Found at i:4938 original size:30 final size:30
Alignment explanation
Indices: 4902--4973 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
4892 TAATGAAGAG
4902 TGTATCGATACATCTAGGTAAAACCTAGAA
1 TGTATCGATACATCTAGGTAAAACCTAGAA
* *
4932 TGTATCGATACATCTAGGTAAAGCTTAGAA
1 TGTATCGATACATCTAGGTAAAACCTAGAA
4962 TGTATCGATACA
1 TGTATCGATACA
4974 AATTCTGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (30 bp):
TGTATCGATACATCTAGGTAAAACCTAGAA
Found at i:5664 original size:21 final size:21
Alignment explanation
Indices: 5613--5674 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
5603 CTCCAGTGAA
* *
5613 ATTAGTTACCGTAGTGATGAG
1 ATTAGATATCGTAGTGATGAG
*
5634 ATTAGGTATCGTAGTGATGAG
1 ATTAGATATCGTAGTGATGAG
*
5655 ATT-GAATATCGTAATGATGA
1 ATTAG-ATATCGTAGTGATGA
5675 TATCAAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.34
Consensus pattern (21 bp):
ATTAGATATCGTAGTGATGAG
Found at i:5914 original size:36 final size:36
Alignment explanation
Indices: 5781--5920 Score: 90
Period size: 37 Copynumber: 3.8 Consensus size: 36
5771 GTGTATATAT
* * *
5781 AATAA-ATAATTAAAAGTTATATCTATAGT--AAATA
1 AATAATATAATTATAA-TTATATTTATATTAAAAATA
* *
5815 AATAAAATATAAATAATAATTATATTTATCTTAAACAATA
1 AAT--AATAT-AATTATAATTATATTTATATTAAA-AATA
* * * **
5855 AATTAAAATTATTAAAAGCATATTT-TATTAAAAATA
1 AA-TAATATAATTATAATTATATTTATATTAAAAATA
*
5891 AATAATTATAATTATAATTATATTCATATT
1 AATAA-TATAATTATAATTATATTTATATT
5921 TATATTTATA
Statistics
Matches: 78, Mismatches: 18, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
34 3 0.04
35 3 0.04
36 21 0.27
37 22 0.28
38 17 0.22
39 5 0.06
40 6 0.08
41 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (36 bp):
AATAATATAATTATAATTATATTTATATTAAAAATA
Found at i:5959 original size:17 final size:17
Alignment explanation
Indices: 5937--5986 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
5927 TATATGAATT
5937 AATAAATATATATTAAA
1 AATAAATATATATTAAA
5954 AATAAAT-TAATAATATAAA
1 AATAAATAT-AT-AT-TAAA
5973 AATTAAA-ATATATT
1 AA-TAAATATATATT
5987 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
16 1 0.04
17 10 0.36
18 4 0.14
19 8 0.29
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAAATATATATTAAA
Found at i:5974 original size:20 final size:21
Alignment explanation
Indices: 5941--5979 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5931 TGAATTAATA
*
5941 AATATATATTAAAAATAAATT
1 AATATATATAAAAAATAAATT
*
5962 AATA-ATATAAAAATTAAA
1 AATATATATAAAAAATAAA
5980 ATATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATATATAAAAAATAAATT
Found at i:13367 original size:20 final size:20
Alignment explanation
Indices: 13339--13406 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 20
13329 AATTAAATTT
13339 TTTATTTATAAATTAAATA-AA
1 TTTATTTAT-AA-TAAATATAA
13360 TTTA-TTATAATAAATATAA
1 TTTATTTATAATAAATATAA
* *
13379 TTTAAATATATAATAAAAATAA
1 TTT--ATTTATAATAAATATAA
13401 -TTATTT
1 TTTATTT
13407 TTTTATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 6 0.15
19 10 0.25
20 4 0.10
21 7 0.17
22 13 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTATTTATAATAAATATAA
Found at i:13430 original size:24 final size:24
Alignment explanation
Indices: 13399--13444 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
13389 TAATAAAAAT
*
13399 AATTATTT-TTTTATAAATTTTAAA
1 AATTATTTATATT-TAAATTTTAAA
13423 AATTATTTATATTTAAATTTTA
1 AATTATTTATATTTAAATTTTA
13445 TATATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATTATTTATATTTAAATTTTAAA
Found at i:13814 original size:18 final size:20
Alignment explanation
Indices: 13787--13830 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
13777 TTTAAAATTT
*
13787 ATATAATATAAATTAT-T-A
1 ATATATTATAAATTATATAA
*
13805 ATATATTATAATTTATATAA
1 ATATATTATAAATTATATAA
13825 ATATAT
1 ATATAT
13831 AATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 1 0.05
20 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATTATAAATTATATAA
Found at i:13822 original size:27 final size:26
Alignment explanation
Indices: 13792--13859 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 26
13782 AATTTATATA
13792 ATATAAAT-TATTAATATATTATAATTT
1 ATATAAATATA-TAATATATTA-AATTT
*
13819 ATATAAATATATAATATTTTAAATTT
1 ATATAAATATATAATATATTAAATTT
13845 A-ATTATAATATATAA
1 ATA-TA-AATATATAA
13860 AAATATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 8 0.22
27 26 0.70
28 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATAAATATATAATATATTAAATTT
Found at i:14226 original size:13 final size:13
Alignment explanation
Indices: 14208--14232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14198 AGATTTAAAT
14208 TTTTTTATATTTA
1 TTTTTTATATTTA
14221 TTTTTTATATTT
1 TTTTTTATATTT
14233 TTGTTAGGTA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTATATTTA
Found at i:14734 original size:3 final size:3
Alignment explanation
Indices: 14726--14762 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
14716 GAATAGTTTA
* *
14726 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT GAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
14763 TAGTACTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:15456 original size:28 final size:25
Alignment explanation
Indices: 15414--15468 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
15404 ATTAATTAAA
15414 ATTATTATTTATTAATTA-AAATAAT
1 ATTATTATTTATTAATTATAAA-AAT
15439 ATTATTATTTAAATTTAATTATAAAAAT
1 ATTATTATTT--A-TTAATTATAAAAAT
15467 AT
1 AT
15469 AAATATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 10 0.38
27 1 0.04
28 12 0.46
29 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTATTATTTATTAATTATAAAAAT
Found at i:15462 original size:25 final size:23
Alignment explanation
Indices: 15402--15463 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
15392 TCTGTAAATA
15402 AAATTAATTA-AAATTATTATTT
1 AAATTAATTATAAATTATTATTT
*
15424 ATTAATTAA-AATAATATTATTATTT
1 A--AATTAATTATAA-ATTATTATTT
15449 AAATTTAATTATAAA
1 AAA-TTAATTATAAA
15464 AATATAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
22 1 0.03
23 3 0.09
24 13 0.41
25 15 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATTAATTATAAATTATTATTT
Found at i:22575 original size:338 final size:337
Alignment explanation
Indices: 21930--22604 Score: 1215
Period size: 338 Copynumber: 2.0 Consensus size: 337
21920 TACCATGTTC
21930 AGGAAGATTTCCATTTCTCAACAAATTTCTTTTTTGAAAATCAAGCTCAATTTCATGGTGCTTAA
1 AGGAAGATTTCCATTTCTCAACAAATTTCTTTTTTGAAAATCAAGCTCAATTTCATGGTGCTTAA
* *
21995 TTGAAACAGAAATACCATGTCTGAGCTATTTTATTCTTACACTTCATTTTCTTTTTAAAGTTTTT
66 TTGAAACAGAAATACCATATCTGAGCTATTTTATTCTTACACTTCATTTTCTTTATAAAGTTTTT
* *
22060 GCGTTTGACATCTGACACATTTGGACATTGGTATGGGGAAAACTTTTAAAAAATTGAATGTACTT
131 GCATTTGACATCTGACACATTTGGACATTGGTATGGGGAAAACTTTTAAAAAATTGAATATACTT
**
22125 GTGTCCAATACTTATTTGCATCCAACACTCTTCCTCCAGTCCATGTAACATGGCATCTAAGTGAT
196 GTGTCCAATACTTACCTGCATCCAACACTCTTCCTCCAGTCCATGTAACATGGCATCTAAGTGAT
22190 TATGACCAAAGAAATTTGTCAAAATAGTGTCTGCTCAAAAGGTTCAAATTTCAATGCCGCTTGGG
261 TATGACCAAAGAAATTTGTCAAAATAGTGTCTGCTCAAAAGGTTCAAATTTCAATGCCGCTTGGG
22255 AGATTGAGGATT
326 AGATTGAGGATT
*
22267 AGGAAGATTTCCATTTCTCAACAAATTTCTTTTTTTGAAAATCAAGCTCAATTTCATGGTTCTTA
1 AGGAAGATTTCCATTTCTCAACAAATTTC-TTTTTTGAAAATCAAGCTCAATTTCATGGTGCTTA
22332 ATTGAAACAGAAATACCATATCTGAGCTATTTTATTCTTACACTTCATTTTCTTTATAAAGTTTT
65 ATTGAAACAGAAATACCATATCTGAGCTATTTTATTCTTACACTTCATTTTCTTTATAAAGTTTT
* *
22397 TGCATTTGACGTCTGACACATTTGGACATTGGTTTGGGGAAAACTTTTAAAAAATTGAATATACT
130 TGCATTTGACATCTGACACATTTGGACATTGGTATGGGGAAAACTTTTAAAAAATTGAATATACT
* *
22462 TGTGTCTAATACTTACCTGCATCCGACACTCTTCCTCCAGTCCATGTAACATGGCATCTAAGTGA
195 TGTGTCCAATACTTACCTGCATCCAACACTCTTCCTCCAGTCCATGTAACATGGCATCTAAGTGA
** *
22527 TTATGACTTAAGAAATTTGTCAAAATAGTTTCTGCTCAAAAGGTTCAAATTTCAATGCCGCTTGG
260 TTATGACCAAAGAAATTTGTCAAAATAGTGTCTGCTCAAAAGGTTCAAATTTCAATGCCGCTTGG
22592 GAGATTGAGGATT
325 GAGATTGAGGATT
22605 GCTAATTTTA
Statistics
Matches: 323, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
337 29 0.09
338 294 0.91
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (337 bp):
AGGAAGATTTCCATTTCTCAACAAATTTCTTTTTTGAAAATCAAGCTCAATTTCATGGTGCTTAA
TTGAAACAGAAATACCATATCTGAGCTATTTTATTCTTACACTTCATTTTCTTTATAAAGTTTTT
GCATTTGACATCTGACACATTTGGACATTGGTATGGGGAAAACTTTTAAAAAATTGAATATACTT
GTGTCCAATACTTACCTGCATCCAACACTCTTCCTCCAGTCCATGTAACATGGCATCTAAGTGAT
TATGACCAAAGAAATTTGTCAAAATAGTGTCTGCTCAAAAGGTTCAAATTTCAATGCCGCTTGGG
AGATTGAGGATT
Found at i:26751 original size:18 final size:18
Alignment explanation
Indices: 26724--26764 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
26714 ATTTTTATTA
*
26724 TGAAATGATTTATACTAT
1 TGAAAGGATTTATACTAT
*
26742 TGAAAGGATTTTTACTAT
1 TGAAAGGATTTATACTAT
*
26760 GGAAA
1 TGAAA
26765 AGAATATGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (18 bp):
TGAAAGGATTTATACTAT
Found at i:27339 original size:16 final size:16
Alignment explanation
Indices: 27240--27341 Score: 55
Period size: 16 Copynumber: 6.0 Consensus size: 16
27230 TCATAATTCA
*
27240 AGGATATTTAGAAAATC
1 AGGAAATTTAG-AAATC
*
27257 AAGAAATTTCA-AAATC
1 AGGAAATTT-AGAAATC
* * *
27273 AGGAAATTTA-CAGTT
1 AGGAAATTTAGAAATC
*
27288 ATGGAAATCCGTAGAAATC
1 A-GGAAAT--TTAGAAATC
*
27307 AAGAAATGTGCTAGAAATC
1 AGGAAAT-T--TAGAAATC
27326 AGGAAATTTAGAAATC
1 AGGAAATTTAGAAATC
27342 TACACTCCCC
Statistics
Matches: 64, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
15 4 0.06
16 27 0.42
17 7 0.11
18 9 0.14
19 17 0.27
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (16 bp):
AGGAAATTTAGAAATC
Found at i:41048 original size:2 final size:2
Alignment explanation
Indices: 41043--41067 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41033 AAATTGGCCA
41043 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
41068 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:41867 original size:20 final size:19
Alignment explanation
Indices: 41842--41911 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
41832 GAAATGCTTG
*
41842 TATGTAATTCTTAATATTTA
1 TATGTAATTATTAAT-TTTA
*
41862 TATGTAATTTTTAATTTTA
1 TATGTAATTATTAATTTTA
* * *
41881 TGTATAATTAAATAATGTTTA
1 TATGTAATT-ATTAAT-TTTA
41902 TATGTAATTA
1 TATGTAATTA
41912 CATGTAAATG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 11 0.27
20 19 0.46
21 11 0.27
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.54
Consensus pattern (19 bp):
TATGTAATTATTAATTTTA
Found at i:41888 original size:19 final size:20
Alignment explanation
Indices: 41846--41889 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
41836 TGCTTGTATG
*
41846 TAATTCTTAATATTTATATG
1 TAATTCTTAATATTTATATA
* *
41866 TAATTTTTAAT-TTTATGTA
1 TAATTCTTAATATTTATATA
41885 TAATT
1 TAATT
41890 AAATAATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (20 bp):
TAATTCTTAATATTTATATA
Found at i:41902 original size:21 final size:20
Alignment explanation
Indices: 41873--41911 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
41863 ATGTAATTTT
*
41873 TAATTTTATGTATAATTAAA
1 TAATTTTATATATAATTAAA
*
41893 TAATGTTTATATGTAATTA
1 TAAT-TTTATATATAATTA
41912 CATGTAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TAATTTTATATATAATTAAA
Found at i:43325 original size:16 final size:16
Alignment explanation
Indices: 43306--43340 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43296 GATTCAAATA
43306 AAAAATAATTAAATTT
1 AAAAATAATTAAATTT
**
43322 AAAAATTTTTAAATTT
1 AAAAATAATTAAATTT
43338 AAA
1 AAA
43341 TTAATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAATAATTAAATTT
Found at i:44478 original size:29 final size:29
Alignment explanation
Indices: 44418--44478 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
44408 TAACAAAAAA
*
44418 ATACCAATCAATATTCCAATAATTACATT
1 ATACCAATCAATATTCCAATAATTACAAT
44447 ATACCAATCAATATATTCCAATAA-T-CAAT
1 ATACCAATC-A-ATATTCCAATAATTACAAT
44476 ATA
1 ATA
44479 TACTACATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 15 0.52
30 2 0.07
31 12 0.41
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.33
Consensus pattern (29 bp):
ATACCAATCAATATTCCAATAATTACAAT
Found at i:44481 original size:31 final size:29
Alignment explanation
Indices: 44418--44481 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 29
44408 TAACAAAAAA
*
44418 ATACCAATCAATATTCCAATAATTACATT
1 ATACCAATCAATATTCCAATAATCACATT
44447 ATACCAATCAATATATTCCAATAATCA-ATAT
1 ATACCAATC-A-ATATTCCAATAATCACAT-T
44478 ATAC
1 ATAC
44482 TACATTCATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.29
30 3 0.10
31 19 0.61
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (29 bp):
ATACCAATCAATATTCCAATAATCACATT
Found at i:46050 original size:21 final size:21
Alignment explanation
Indices: 45999--46050 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
45989 AAAAATATTT
*
45999 TTTATTTAAATTTAATTAATA
1 TTTATTTAAAATTAATTAATA
*
46020 TTTATATAAAATTAATTTAATA
1 TTTATTTAAAATTAA-TTAATA
46042 TTT-TTTAAA
1 TTTATTTAAA
46051 TAGTGATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTATTTAAAATTAATTAATA
Found at i:52320 original size:2 final size:2
Alignment explanation
Indices: 52313--52337 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52303 TTAACTTTGC
52313 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 T
52338 GTATGTGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53794 original size:12 final size:12
Alignment explanation
Indices: 53777--53811 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
53767 AATACTGGGC
53777 TGATTCTGGTTA
1 TGATTCTGGTTA
53789 TGATTCTGGTTA
1 TGATTCTGGTTA
53801 TGATTCTGGTT
1 TGATTCTGGTT
53812 CATGTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.14, C:0.09, G:0.26, T:0.51
Consensus pattern (12 bp):
TGATTCTGGTTA
Found at i:59310 original size:3 final size:3
Alignment explanation
Indices: 59302--59330 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
59292 AGAATTTTTC
59302 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
59331 ATTCATGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:61080 original size:9 final size:9
Alignment explanation
Indices: 61062--61093 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
61052 ATATCCTTTC
61062 ATAA-AAAA
1 ATAATAAAA
61070 ATAATAAAA
1 ATAATAAAA
61079 ATAATAAAA
1 ATAATAAAA
61088 ATAATA
1 ATAATA
61094 TAATTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
ATAATAAAA
Found at i:67010 original size:30 final size:30
Alignment explanation
Indices: 66953--67010 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
66943 ATAATCTTAA
* **
66953 ATTAGTGTTTGTTTTAATCTTAGCTAGATT
1 ATTAGTGTTTATTTTAATCCAAGCTAGATT
66983 ATTAGTGTTTATTTT-ATCCAAGACTAGA
1 ATTAGTGTTTATTTTAATCCAAG-CTAGA
67011 CTACTAGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.48
Consensus pattern (30 bp):
ATTAGTGTTTATTTTAATCCAAGCTAGATT
Found at i:67475 original size:3 final size:3
Alignment explanation
Indices: 67462--67497 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
67452 TCAATATGTT
*
67462 TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
67498 GAATTGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:68162 original size:4 final size:4
Alignment explanation
Indices: 68155--68182 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
68145 AAGAAATGAG
68155 ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT
68183 GTGCTAACTT
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:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:69613 original size:20 final size:22
Alignment explanation
Indices: 69568--69614 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
69558 AAACTGAGTT
69568 TTTTGTTTCTATTCTTTTTCT-
1 TTTTGTTTCTATTCTTTTTCTG
*
69589 TTTTTTTTC-ATTCTTTATT-TG
1 TTTTGTTTCTATTCTTT-TTCTG
69610 TTTTG
1 TTTTG
69615 ATACTACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTTGTTTCTATTCTTTTTCTG
Found at i:70502 original size:41 final size:40
Alignment explanation
Indices: 70426--70507 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
70416 TTTTTTTTCT
* *
70426 AGAGTCAGGCACATTGTTACAAAAGCTAGGCAAACATGAC
1 AGAGTCAAGCACATTATTACAAAAGCTAGGCAAACATGAC
* *
70466 AGAGTCAAGCACATTTATTACAAGAGCTAGGTAAACATGAC
1 AGAGTCAAGCACA-TTATTACAAAAGCTAGGCAAACATGAC
70507 A
1 A
70508 CATACGCTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 12 0.32
41 25 0.68
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (40 bp):
AGAGTCAAGCACATTATTACAAAAGCTAGGCAAACATGAC
Done.