Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold411
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: 134893
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:486 original size:14 final size:15
Alignment explanation
Indices: 451--490 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
441 AATATTTACA
451 TAAAAATTAAACTAAG
1 TAAAAA-TAAACTAAG
*
467 TAAAAATAAA-TAAT
1 TAAAAATAAACTAAG
481 TAAAAATAAA
1 TAAAAATAAA
491 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (15 bp):
TAAAAATAAACTAAG
Found at i:2847 original size:14 final size:15
Alignment explanation
Indices: 2811--2851 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
2801 GAATATTTAC
2811 ATAAAAATTAAACTAA
1 ATAAAAA-TAAACTAA
*
2827 GTAAAAATAAA-TAA
1 ATAAAAATAAACTAA
2841 ATAAAAATAAA
1 ATAAAAATAAA
2852 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAACTAA
Found at i:9146 original size:14 final size:15
Alignment explanation
Indices: 9111--9150 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
9101 AATATTTACA
9111 TAAAAATTAAACTAAG
1 TAAAAA-TAAACTAAG
*
9127 TAAAAATAAA-TAAT
1 TAAAAATAAACTAAG
9141 TAAAAATAAA
1 TAAAAATAAA
9151 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (15 bp):
TAAAAATAAACTAAG
Found at i:11518 original size:14 final size:15
Alignment explanation
Indices: 11482--11522 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
11472 GAATATTTAC
11482 ATAAAAATTAAACTAA
1 ATAAAAA-TAAACTAA
*
11498 GTAAAAATAAA-TAA
1 ATAAAAATAAACTAA
11512 ATAAAAATAAA
1 ATAAAAATAAA
11523 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAACTAA
Found at i:19600 original size:27 final size:28
Alignment explanation
Indices: 19555--19618 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
19545 AGTAGATTCG
**
19555 TGAAAAAAAAATTTGAAAAAAAAAGAAA
1 TGAAAAAAAAATTCAAAAAAAAAAGAAA
**
19583 TCGAAAAAAAAA-TC-AAAAAAATTGAAA
1 T-GAAAAAAAAATTCAAAAAAAAAAGAAA
19610 TGAAAAAAA
1 TGAAAAAAA
19619 TTGTATACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 8 0.25
27 12 0.38
28 2 0.06
29 10 0.31
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.14
Consensus pattern (28 bp):
TGAAAAAAAAATTCAAAAAAAAAAGAAA
Found at i:19610 original size:15 final size:15
Alignment explanation
Indices: 19592--19621 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19582 ATCGAAAAAA
19592 AAATCAAAAAAATTG
1 AAATCAAAAAAATTG
*
19607 AAATGAAAAAAATTG
1 AAATCAAAAAAATTG
19622 TATACGGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.20
Consensus pattern (15 bp):
AAATCAAAAAAATTG
Found at i:25585 original size:17 final size:18
Alignment explanation
Indices: 25563--25603 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
25553 CGTTTCTTTT
25563 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
25580 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
25598 T-TTTTG
1 TCTTTTG
25604 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:25587 original size:24 final size:25
Alignment explanation
Indices: 25534--25587 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
25524 AACAAATTCT
* *
25534 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
25559 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
25582 TTTTTT
1 TTTTTT
25588 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:27882 original size:1 final size:1
Alignment explanation
Indices: 27839--27870 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
27829 CCGTATGCAA
*
27839 TTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27871 AACTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:32231 original size:24 final size:25
Alignment explanation
Indices: 32178--32231 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
32168 AACAAATTCT
* *
32178 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
32203 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
32226 TTTTTT
1 TTTTTT
32232 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:34509 original size:15 final size:14
Alignment explanation
Indices: 34480--34508 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34470 CTAGACCGTA
34480 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
34494 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
34508 T
1 T
34509 TTTTTTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:34511 original size:21 final size:21
Alignment explanation
Indices: 34485--34528 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
34475 CCGTATGCAA
*
34485 TTTTTTTTTTGCA-ATTTTTT
1 TTTTTTTTTTTCAGATTTTTT
34505 TTTTTTTTTTTCAGATTTTTT
1 TTTTTTTTTTTCAGATTTTTT
34526 TTT
1 TTT
34529 AAACTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.09, C:0.05, G:0.05, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTTTCAGATTTTTT
Found at i:34536 original size:12 final size:12
Alignment explanation
Indices: 34521--34552 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
34511 TTTTTCAGAT
34521 TTTTTTTTAAAC
1 TTTTTTTTAAAC
*
34533 TTTTTTTTTAAC
1 TTTTTTTTAAAC
34545 TTTTTTTT
1 TTTTTTTT
34553 TCGAAGCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTTTAAAC
Found at i:34553 original size:12 final size:13
Alignment explanation
Indices: 34507--34553 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
34497 AATTTTTTTT
*
34507 TTTTTTTTTCAGA-
1 TTTTTTTTT-AAAC
34520 TTTTTTTTTAAAC
1 TTTTTTTTTAAAC
34533 TTTTTTTTT-AAC
1 TTTTTTTTTAAAC
34545 TTTTTTTTT
1 TTTTTTTTT
34554 CGAAGCTACG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 14 0.44
13 18 0.56
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTAAAC
Found at i:38901 original size:17 final size:18
Alignment explanation
Indices: 38879--38919 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
38869 CGTTTCTTTT
38879 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
38896 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
38914 T-TTTTG
1 TCTTTTG
38920 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:38903 original size:24 final size:25
Alignment explanation
Indices: 38850--38903 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
38840 AACAAATTCT
* *
38850 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
38875 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
38898 TTTTTT
1 TTTTTT
38904 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:41179 original size:18 final size:18
Alignment explanation
Indices: 41156--41195 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41146 CCGTATGCAA
41156 TTTTTTTTTTGCAATTTT
1 TTTTTTTTTTGCAATTTT
* *
41174 TTTTTTTTTTTCGATTTT
1 TTTTTTTTTTGCAATTTT
41192 TTTT
1 TTTT
41196 CAAACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTTGCAATTTT
Found at i:41180 original size:15 final size:14
Alignment explanation
Indices: 41151--41179 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41141 CTAGACCGTA
41151 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
41165 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
41179 T
1 T
41180 TTTTTCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:43437 original size:17 final size:15
Alignment explanation
Indices: 43400--43438 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
43390 TATCTCCCAC
43400 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
43416 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
43433 TCATTT
1 TCATTT
43439 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:44327 original size:26 final size:30
Alignment explanation
Indices: 44288--44351 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 30
44278 CAATCACTCT
44288 TTTTTTTTTCAATT-TCG-A-TTTTTT-TTC
1 TTTTTTTTTCAATTCT-GAATTTTTTTATTC
44315 TTTTTTTTT-AATTCTGAATTTTTTTATTC
1 TTTTTTTTTCAATTCTGAATTTTTTTATTC
44344 TTTTTTTT
1 TTTTTTTT
44352 CTTCAATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.15
27 11 0.33
28 6 0.18
29 11 0.33
ACGTcount: A:0.12, C:0.08, G:0.03, T:0.77
Consensus pattern (30 bp):
TTTTTTTTTCAATTCTGAATTTTTTTATTC
Found at i:44335 original size:27 final size:29
Alignment explanation
Indices: 44288--44351 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
44278 CAATCACTCT
44288 TTTTTTTTTCAATTTCGA-TTTTTT-TTC
1 TTTTTTTTTCAATTTCGATTTTTTTATTC
44315 TTTTTTTTT-AA-TTCTGAATTTTTTTATTC
1 TTTTTTTTTCAATTTC-G-ATTTTTTTATTC
44344 TTTTTTTT
1 TTTTTTTT
44352 CTTCAATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 3 0.09
26 3 0.09
27 10 0.30
28 6 0.18
29 11 0.33
ACGTcount: A:0.12, C:0.08, G:0.03, T:0.77
Consensus pattern (29 bp):
TTTTTTTTTCAATTTCGATTTTTTTATTC
Found at i:44413 original size:11 final size:11
Alignment explanation
Indices: 44397--44447 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
44387 AATACAAACT
44397 TTTTTTTTGAA
1 TTTTTTTTGAA
44408 TTTTTTTTGAA
1 TTTTTTTTGAA
*
44419 TTTTTTTTCAA
1 TTTTTTTTGAA
44430 GTTTTTTTT--A
1 -TTTTTTTTGAA
44440 TTTTTTTT
1 TTTTTTTT
44448 ACAATACCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
9 8 0.21
10 1 0.03
11 21 0.55
12 8 0.21
ACGTcount: A:0.14, C:0.02, G:0.06, T:0.78
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:44712 original size:20 final size:20
Alignment explanation
Indices: 44689--44734 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
44679 CCAGCTCGAA
*
44689 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
44709 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
44729 TTAGCT
1 TTAGCT
44735 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:44716 original size:30 final size:30
Alignment explanation
Indices: 44681--44754 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
44671 AGTTTTTCCC
44681 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
44711 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
44741 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
44755 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:53201 original size:6 final size:6
Alignment explanation
Indices: 53168--53275 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
53158 AAAGAAATTG
* * * ** *
53168 AAAG-A AAACAA AAAGAA AATGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
53215 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
53266 AAAGAA AAAG
1 AAAGAA AAAG
53276 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 26, Indels: 7
0.69 0.25 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.81
7 7 0.10
8 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:53216 original size:57 final size:55
Alignment explanation
Indices: 53155--53275 Score: 138
Period size: 57 Copynumber: 2.1 Consensus size: 55
53145 GAAAGAGATT
* *
53155 GAAAAAGAAATTGAAAGAA-A-ACAAAAAGAAAATGAAGAAGAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAA-AAGAGACAAAAAGAAAATGAAG-A-AAAAA-AAATTGAAAAA
* *
53212 GAAAAAGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAA
1 GAAAAAGAAATCGAAAAA--GAGACAAAAAGAAAATGAAGAAAAAAAAATTGAAAAA
53269 GAAAAAG
1 GAAAAAG
53276 CGAAAAAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 2 0.04
57 32 0.57
58 4 0.07
59 2 0.04
60 16 0.29
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.08
Consensus pattern (55 bp):
GAAAAAGAAATCGAAAAAGAGACAAAAAGAAAATGAAGAAAAAAAAATTGAAAAA
Found at i:53229 original size:18 final size:17
Alignment explanation
Indices: 53154--53230 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 17
53144 AGAAAGAGAT
**
53154 TGAAAAAGAAATTGAAA
1 TGAAAAAGAAAAAGAAA
*
53171 -G-AAAACAAAAAGAAAA
1 TGAAAAAGAAAAAG-AAA
*
53187 TGAAGAAGAAAAAGAAA
1 TGAAAAAGAAAAAGAAA
*
53204 TTGCAAAAGAAAAAGAAA
1 -TGAAAAAGAAAAAGAAA
53222 TCGAAAAAG
1 T-GAAAAAG
53231 TGAGAGAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
15 8 0.17
16 4 0.09
17 5 0.11
18 30 0.64
ACGTcount: A:0.69, C:0.04, G:0.18, T:0.09
Consensus pattern (17 bp):
TGAAAAAGAAAAAGAAA
Found at i:53257 original size:14 final size:13
Alignment explanation
Indices: 53236--53273 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
53226 AAAAGTGAGA
53236 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
53248 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
53263 GAAAAAGAAAA
1 GAAAAAGAAAA
53274 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:53287 original size:21 final size:21
Alignment explanation
Indices: 53237--53287 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
53227 AAAGTGAGAG
*
53237 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
53258 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
53279 AAAAAGAAA
1 AAAAAGAAA
53288 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:53291 original size:27 final size:27
Alignment explanation
Indices: 53189--53293 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 27
53179 AAAGAAAATG
* *
53189 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*** **
53216 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAG-AA--GAAAAAAAAATTGAAAAAGAAA
* *
53246 ATGAAGAAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*
53273 AAG-CGAAAAAAGAAATTGAAA
1 AAGAAGAAAAAA-AAATTGAAA
53294 GAGAGCTTGA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
26 6 0.10
27 30 0.51
28 2 0.03
29 2 0.03
30 19 0.32
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (27 bp):
AAGAAGAAAAAAAAATTGAAAAAGAAA
Found at i:53327 original size:33 final size:33
Alignment explanation
Indices: 53290--53352 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
53280 AAAAGAAATT
53290 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
53323 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
53353 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:55151 original size:20 final size:20
Alignment explanation
Indices: 55128--55181 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
55118 AGTTTTTCCC
*
55128 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
55148 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
55168 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
55182 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:55163 original size:30 final size:30
Alignment explanation
Indices: 55128--55201 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
55118 AGTTTTTCCC
55128 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
55158 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
55188 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
55202 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:55191 original size:20 final size:20
Alignment explanation
Indices: 55128--55192 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
55118 AGTTTTTCCC
* * * *
55128 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
55148 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
55167 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
55188 AGCTC
1 AGCTC
55193 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:58352 original size:20 final size:20
Alignment explanation
Indices: 58327--58373 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
58317 AAATTGAGTT
*
58327 GAATGAGCTGACTTGAGCAC
1 GAATGAGCTAACTTGAGCAC
*
58347 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
58367 GAATGAG
1 GAATGAG
58374 TTGAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:69743 original size:21 final size:23
Alignment explanation
Indices: 69698--69744 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
69688 TCACCTGCAA
* *
69698 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
69721 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
69742 TAA
1 TAA
69745 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:75117 original size:17 final size:15
Alignment explanation
Indices: 75065--75122 Score: 89
Period size: 15 Copynumber: 3.7 Consensus size: 15
75055 TAGCTTCGTC
75065 TTTTTTTTTCACGAAAA
1 TTTTTTTTTCACG--AA
*
75082 ATTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
75097 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
75112 TTTTTTTTTCA
1 TTTTTTTTTCA
75123 ACTTGATATC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
15 27 0.69
17 12 0.31
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.60
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:75177 original size:12 final size:12
Alignment explanation
Indices: 75160--75206 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
75150 ATGGAAACCA
75160 AATTTTTTTTTG
1 AATTTTTTTTTG
75172 AATTTTTTTTT-
1 AATTTTTTTTTG
75183 -A-TTTTTTTTG
1 AATTTTTTTTTG
*
75193 AAATTTTTTTTG
1 AATTTTTTTTTG
75205 AA
1 AA
75207 AAAACTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.25
10 1 0.03
11 1 0.03
12 22 0.69
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:75189 original size:22 final size:21
Alignment explanation
Indices: 75163--75203 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
75153 GAAACCAAAT
*
75163 TTTTTTTTGAATTTTTTTTTA
1 TTTTTTTTGAAATTTTTTTTA
75184 TTTTTTTTGAAATTTTTTTT
1 TTTTTTTTGAAATTTTTTTT
75204 GAAAAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTTTTGAAATTTTTTTTA
Found at i:75207 original size:12 final size:11
Alignment explanation
Indices: 75163--75206 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
75153 GAAACCAAAT
75163 TTTTTTTTGAA
1 TTTTTTTTGAA
*
75174 TTTTTTTT-TA
1 TTTTTTTTGAA
75184 TTTTTTTTGAAA
1 TTTTTTTTG-AA
75196 TTTTTTTTGAA
1 TTTTTTTTGAA
75207 AAAACTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 9 0.31
11 10 0.34
12 10 0.34
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:76240 original size:21 final size:23
Alignment explanation
Indices: 76195--76241 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
76185 TCACCTGCAA
* *
76195 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
76218 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
76239 TAA
1 TAA
76242 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:81330 original size:10 final size:10
Alignment explanation
Indices: 81315--81352 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
81305 TTGGGTTAAG
81315 ATTGAGCTGA
1 ATTGAGCTGA
81325 ATTGAGCTCGA
1 ATTGAGCT-GA
81336 A-TGAGCTGA
1 ATTGAGCTGA
*
81345 CTTGAGCT
1 ATTGAGCT
81353 TGAGTGAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:92803 original size:16 final size:15
Alignment explanation
Indices: 92765--92804 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
92755 GAATGTGATT
92765 TTGGAAAAAATTTTG
1 TTGGAAAAAATTTTG
**
92780 TTAAAAAAAATTTTTG
1 TTGGAAAAAA-TTTTG
92796 TTGGAAAAA
1 TTGGAAAAA
92805 TTTCACTGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (15 bp):
TTGGAAAAAATTTTG
Found at i:94824 original size:46 final size:46
Alignment explanation
Indices: 94771--94864 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
94761 CAAAGAAAAG
* *
94771 ACCTCGACCCATTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
94817 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
94863 AC
1 AC
94865 GCCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:97590 original size:19 final size:18
Alignment explanation
Indices: 97554--97593 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
97544 TTTCCACTCG
*
97554 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
97572 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
97591 TTT
1 TTT
97594 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:98665 original size:13 final size:13
Alignment explanation
Indices: 98647--98690 Score: 63
Period size: 14 Copynumber: 3.4 Consensus size: 13
98637 ACTAGCTCTC
98647 TTTTTTTTTACAA
1 TTTTTTTTTACAA
98660 TTTTTTTTTCACAA
1 TTTTTTTTT-ACAA
*
98674 TTTTTTTTCA-AA
1 TTTTTTTTTACAA
98686 TTTTT
1 TTTTT
98691 CACAACTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 7 0.24
13 10 0.34
14 12 0.41
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTTTTACAA
Found at i:98666 original size:14 final size:14
Alignment explanation
Indices: 98647--98690 Score: 67
Period size: 13 Copynumber: 3.4 Consensus size: 14
98637 ACTAGCTCTC
98647 TTTTTTTTT-ACAA
1 TTTTTTTTTCACAA
98660 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
98674 -TTTTTTTTCA-AA
1 TTTTTTTTTCACAA
98686 TTTTT
1 TTTTT
98691 CACAACTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.07
13 23 0.79
14 4 0.14
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:98750 original size:12 final size:12
Alignment explanation
Indices: 98733--98780 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
98723 GGAAACTAGT
98733 TTTTTTTTCGAA
1 TTTTTTTTCGAA
*
98745 TTTTTTTTTGAAA
1 TTTTTTTTCG-AA
* *
98758 TTTTTTTTTGAG
1 TTTTTTTTCGAA
98770 TTTTTTTTCGA
1 TTTTTTTTCGA
98781 GAAACTACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
12 20 0.62
13 12 0.38
ACGTcount: A:0.15, C:0.04, G:0.10, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:98750 original size:13 final size:12
Alignment explanation
Indices: 98732--98777 Score: 65
Period size: 13 Copynumber: 3.7 Consensus size: 12
98722 TGGAAACTAG
98732 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
98745 TTTTTTTTTGAAA
1 TTTTTTTTTG-AA
*
98758 TTTTTTTTTGAG
1 TTTTTTTTTGAA
98770 TTTTTTTT
1 TTTTTTTT
98778 CGAGAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.13, C:0.02, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:101828 original size:22 final size:22
Alignment explanation
Indices: 101800--101863 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
101790 CCTTTTTGAA
*
101800 CCATTACCATTTTGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
*
101822 CCATTACCATTTCGTACCAGAT
1 CCATTACCATTTCGTACCAAAT
* *
101844 CCCTTACCATTTCATACCAA
1 CCATTACCATTTCGTACCAA
101864 TTCCCAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:102878 original size:20 final size:21
Alignment explanation
Indices: 102843--102881 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
102833 CAGCTCGTTG
102843 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
102864 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
102882 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:103289 original size:13 final size:13
Alignment explanation
Indices: 103271--103296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
103261 TGTGTCCTAA
103271 TATGAATTAAATT
1 TATGAATTAAATT
103284 TATGAATTAAATT
1 TATGAATTAAATT
103297 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:104424 original size:10 final size:10
Alignment explanation
Indices: 104409--104456 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
104399 GTAAGTGATT
104409 AAAAAAAT-A
1 AAAAAAATAA
**
104418 AAAAAAATTG
1 AAAAAAATAA
104428 AAAAAAATAA
1 AAAAAAATAA
104438 AAAAAAAGTAA
1 AAAAAAA-TAA
104449 AAAAAAAT
1 AAAAAAAT
104457 TCGTGGATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.24
10 16 0.47
11 10 0.29
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.12
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:104450 original size:19 final size:18
Alignment explanation
Indices: 104408--104453 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
104398 AGTAAGTGAT
*
104408 TAAAAAAATAAAAAAAAT
1 TAAAAAAATAAAAAAAAG
104426 TGAAAAAAATAAAAAAAAAG
1 T-AAAAAAAT-AAAAAAAAG
104446 TAAAAAAA
1 TAAAAAAA
104454 AATTCGTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 15 0.60
20 9 0.36
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (18 bp):
TAAAAAAATAAAAAAAAG
Found at i:105197 original size:20 final size:20
Alignment explanation
Indices: 105174--105227 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
105164 AGTTTTTCCC
*
105174 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
105194 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
105214 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
105228 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:105209 original size:30 final size:30
Alignment explanation
Indices: 105174--105247 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
105164 AGTTTTTCCC
105174 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
105204 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
105234 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
105248 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:105237 original size:20 final size:20
Alignment explanation
Indices: 105174--105238 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
105164 AGTTTTTCCC
* * * *
105174 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
105194 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
105213 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
105234 AGCTC
1 AGCTC
105239 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:106849 original size:10 final size:11
Alignment explanation
Indices: 106820--106848 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
106810 ATTTAAAAAA
106820 AAAAAAAATTC
1 AAAAAAAATTC
106831 AAAAAAAATTC
1 AAAAAAAATTC
106842 AAAAAAA
1 AAAAAAA
106849 TCGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:106855 original size:10 final size:10
Alignment explanation
Indices: 106821--106858 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
106811 TTTAAAAAAA
106821 AAAAAAATTC
1 AAAAAAATTC
106831 AAAAAAAATTC
1 -AAAAAAATTC
106842 AAAAAAA-TC
1 AAAAAAATTC
106851 GAAAAAAA
1 -AAAAAAA
106859 AGTGACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 2 0.08
10 14 0.54
11 10 0.38
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:106856 original size:11 final size:12
Alignment explanation
Indices: 106820--106872 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
106810 ATTTAAAAAA
106820 AAAAAAAATTC-
1 AAAAAAAATTCG
106831 AAAAAAAATTC-
1 AAAAAAAATTCG
106842 -AAAAAAA-TCG
1 AAAAAAAATTCG
*
106852 AAAAAAAAGT-G
1 AAAAAAAATTCG
106863 ACAAAAAAAT
1 A-AAAAAAAT
106873 CGAGTTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
9 2 0.05
10 7 0.19
11 20 0.54
12 8 0.22
ACGTcount: A:0.74, C:0.08, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:107938 original size:12 final size:12
Alignment explanation
Indices: 107912--108030 Score: 66
Period size: 12 Copynumber: 9.6 Consensus size: 12
107902 AAAGAAATTG
107912 AAAGAAAAC-AA
1 AAAGAAAACGAA
107923 AAAGAAAACGAA
1 AAAGAAAACGAA
*
107935 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
107947 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
107959 AAAGAAATC-AA
1 AAAGAAAACGAA
* *
107970 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
107982 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
107996 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
108009 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
108024 AAAGAAA
1 AAAGAAA
108031 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 13, Indels: 19
0.72 0.11 0.16
Matches are distributed among these distances:
11 20 0.24
12 28 0.33
13 10 0.12
14 18 0.21
15 8 0.10
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:107942 original size:18 final size:18
Alignment explanation
Indices: 107916--108018 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
107906 AAATTGAAAG
*
107916 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
107934 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
107952 AAAAGAAAAAGAAATC-A
1 AAAAGAAAAAGAAAACGA
** * *
107969 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
107987 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
108008 AAAAGAAAAAG
1 AAAAGAAAAAG
108019 CGAAAAAAGA
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
17 11 0.17
18 34 0.53
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:107944 original size:6 final size:6
Alignment explanation
Indices: 107912--108018 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
107902 AAAGAAATTG
* * ** *
107912 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
107959 AAAG-A AATCAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
108009 AAAGAA AAAG
1 AAAGAA AAAG
108019 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 9
0.69 0.23 0.08
Matches are distributed among these distances:
5 6 0.08
6 56 0.77
7 7 0.10
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:108000 original size:14 final size:13
Alignment explanation
Indices: 107979--108016 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
107969 AAAAGTGAGA
107979 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
107991 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
108006 GAAAAAGAAAA
1 GAAAAAGAAAA
108017 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:108030 original size:21 final size:21
Alignment explanation
Indices: 107980--108030 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
107970 AAAGTGAGAG
*
107980 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
108001 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
108022 AAAAAGAAA
1 AAAAAGAAA
108031 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:108070 original size:33 final size:33
Alignment explanation
Indices: 108033--108095 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
108023 AAAAGAAATT
108033 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
108066 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
108096 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:109892 original size:20 final size:20
Alignment explanation
Indices: 109869--109922 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
109859 AGTTTTTCCC
*
109869 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
109889 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
109909 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
109923 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:109904 original size:30 final size:30
Alignment explanation
Indices: 109869--109942 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
109859 AGTTTTTCCC
109869 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
109899 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
109929 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
109943 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:109932 original size:20 final size:20
Alignment explanation
Indices: 109869--109933 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
109859 AGTTTTTCCC
* * * *
109869 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
109889 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
109908 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
109929 AGCTC
1 AGCTC
109934 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:111767 original size:6 final size:6
Alignment explanation
Indices: 111742--111839 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
111732 TAATGAATTC
** * *
111742 GAAAAA GAAAGT GAAGAA GAAAAA GAAAACA -AAAAA G-AAAA GAAAAC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
** * * *
111789 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
111840 TATGAAAATG
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
5 6 0.09
6 50 0.74
7 8 0.12
8 4 0.06
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:111782 original size:17 final size:17
Alignment explanation
Indices: 111762--111795 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
111752 GTGAAGAAGA
111762 AAAAGAAAACAAAAAAG
1 AAAAGAAAACAAAAAAG
*
111779 AAAAGAAAACGAAAAAG
1 AAAAGAAAACAAAAAAG
111796 TGAGAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAAAAAAG
Found at i:111822 original size:14 final size:13
Alignment explanation
Indices: 111801--111838 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
111791 AAAAGTGAGA
111801 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
111813 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
111828 GAAAAAGAAAA
1 GAAAAAGAAAA
111839 ATATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:111882 original size:17 final size:18
Alignment explanation
Indices: 111857--111896 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
111847 ATGAGATTTC
111857 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
* *
111874 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
111892 AAAAA
1 AAAAA
111897 GAAAGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:111888 original size:18 final size:17
Alignment explanation
Indices: 111857--111906 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
111847 ATGAGATTTC
111857 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
* *
111874 AAAAGCAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
111892 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
111907 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:111912 original size:36 final size:35
Alignment explanation
Indices: 111843--111918 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 35
111833 AGAAAAATAT
111843 GAAAATGAGATTTCAAAAACAAAAGAGAGTGAAAA
1 GAAAATGAGATTTCAAAAACAAAAGAGAGTGAAAA
* *
111878 GCAAAATGAGA-TTGAAAAA-GAAAGAGAGTTTGAAAA
1 G-AAAATGAGATTTCAAAAACAAAAGAGAG--TGAAAA
111914 GAAAA
1 GAAAA
111919 CGAGTGAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
34 8 0.22
35 12 0.33
36 16 0.44
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.14
Consensus pattern (35 bp):
GAAAATGAGATTTCAAAAACAAAAGAGAGTGAAAA
Found at i:111923 original size:17 final size:16
Alignment explanation
Indices: 111858--111923 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 16
111848 TGAGATTTCA
* **
111858 AAAACAAAAGAGAGTG
1 AAAAGAAAAGAGTTTG
*
111874 AAAAGCAAAATGAGATTG
1 AAAAG-AAAA-GAGTTTG
111892 AAAAAGAAAGAGAGTTTG
1 -AAAAGAAA-AGAGTTTG
111910 AAAAGAAAACGAGT
1 AAAAGAAAA-GAGT
111924 GAAGAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
16 5 0.12
17 16 0.38
18 15 0.36
19 6 0.14
ACGTcount: A:0.59, C:0.05, G:0.24, T:0.12
Consensus pattern (16 bp):
AAAAGAAAAGAGTTTG
Found at i:113191 original size:20 final size:21
Alignment explanation
Indices: 113156--113194 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
113146 CAGCTCGTTG
113156 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
113177 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
113195 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:113601 original size:13 final size:13
Alignment explanation
Indices: 113583--113608 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
113573 TGTGTCCTAA
113583 TATGAATTAAATT
1 TATGAATTAAATT
113596 TATGAATTAAATT
1 TATGAATTAAATT
113609 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:115658 original size:11 final size:10
Alignment explanation
Indices: 115642--115671 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
115632 TTCGTAATGT
115642 AAAAAAAAGTC
1 AAAAAAAA-TC
115653 AAAAAAAATC
1 AAAAAAAATC
115663 AAAAAAAAT
1 AAAAAAAAT
115672 TTGAGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:115784 original size:9 final size:10
Alignment explanation
Indices: 115751--115831 Score: 63
Period size: 10 Copynumber: 7.4 Consensus size: 10
115741 GAAGAAATTC
*
115751 AAAAAAAATT
1 AAAAAAAATG
*
115761 CAAAAAAATG
1 AAAAAAAATG
*
115771 AAAAAAAAGG
1 AAAAAAAATG
115781 AAAAAAGAAGTG
1 AAAAAA-AA-TG
115793 AAAAAAAATCG
1 AAAAAAAAT-G
*
115804 AGTTAAAAAAAAG
1 A---AAAAAAATG
115817 AAAAAAAAGTG
1 AAAAAAAA-TG
115828 AAAA
1 AAAA
115832 GTCTTGCGAG
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
10 30 0.53
11 11 0.19
12 7 0.12
13 2 0.04
14 7 0.12
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:116867 original size:12 final size:12
Alignment explanation
Indices: 116841--116959 Score: 66
Period size: 12 Copynumber: 9.6 Consensus size: 12
116831 AAAGAAATTG
116841 AAAGAAAAC-AA
1 AAAGAAAACGAA
116852 AAAGAAAACGAA
1 AAAGAAAACGAA
*
116864 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
116876 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
116888 AAAGAAATC-AA
1 AAAGAAAACGAA
* *
116899 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
116911 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
116925 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
116938 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
116953 AAAGAAA
1 AAAGAAA
116960 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 13, Indels: 19
0.72 0.11 0.16
Matches are distributed among these distances:
11 20 0.24
12 28 0.33
13 10 0.12
14 18 0.21
15 8 0.10
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:116871 original size:18 final size:18
Alignment explanation
Indices: 116845--116947 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
116835 AAATTGAAAG
*
116845 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
116863 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
116881 AAAAGAAAAAGAAATC-A
1 AAAAGAAAAAGAAAACGA
** * *
116898 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
116916 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
116937 AAAAGAAAAAG
1 AAAAGAAAAAG
116948 CGAAAAAAGA
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
17 11 0.17
18 34 0.53
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:116873 original size:6 final size:6
Alignment explanation
Indices: 116841--116947 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
116831 AAAGAAATTG
* * ** *
116841 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
116888 AAAG-A AATCAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
116938 AAAGAA AAAG
1 AAAGAA AAAG
116948 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 9
0.69 0.23 0.08
Matches are distributed among these distances:
5 6 0.08
6 56 0.77
7 7 0.10
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:116929 original size:14 final size:13
Alignment explanation
Indices: 116908--116945 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
116898 AAAAGTGAGA
116908 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
116920 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
116935 GAAAAAGAAAA
1 GAAAAAGAAAA
116946 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:116959 original size:21 final size:21
Alignment explanation
Indices: 116909--116959 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
116899 AAAGTGAGAG
*
116909 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
116930 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
116951 AAAAAGAAA
1 AAAAAGAAA
116960 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:116999 original size:33 final size:33
Alignment explanation
Indices: 116962--117024 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
116952 AAAAGAAATT
116962 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
116995 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
117025 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:118823 original size:20 final size:20
Alignment explanation
Indices: 118800--118853 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
118790 AGTTTTTCCC
*
118800 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
118820 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
118840 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
118854 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:118835 original size:30 final size:30
Alignment explanation
Indices: 118800--118873 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
118790 AGTTTTTCCC
118800 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
118830 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
118860 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
118874 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:118863 original size:20 final size:20
Alignment explanation
Indices: 118800--118864 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
118790 AGTTTTTCCC
* * * *
118800 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
118820 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
118839 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
118860 AGCTC
1 AGCTC
118865 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:120892 original size:13 final size:13
Alignment explanation
Indices: 120874--120899 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
120864 TGTGTCCTAA
120874 TATGAATTAAATT
1 TATGAATTAAATT
120887 TATGAATTAAATT
1 TATGAATTAAATT
120900 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:122965 original size:12 final size:12
Alignment explanation
Indices: 122948--122972 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
122938 AAAAGAGAAG
122948 AAATTCAAAAAA
1 AAATTCAAAAAA
122960 AAATTCAAAAAA
1 AAATTCAAAAAA
122972 A
1 A
122973 TTGAAAAAAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:124072 original size:6 final size:6
Alignment explanation
Indices: 124040--124147 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
124030 AAAGAAATTG
* * ** *
124040 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
124087 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
124138 AAAGAA AAAG
1 AAAGAA AAAG
124148 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:124127 original size:14 final size:13
Alignment explanation
Indices: 124108--124145 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
124098 AAAAGTGAGA
124108 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
124120 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
124135 GAAAAAGAAAA
1 GAAAAAGAAAA
124146 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:124182 original size:12 final size:12
Alignment explanation
Indices: 124151--124182 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
124141 GAAAAAGCGA
*
124151 AAAAAGAATTTG
1 AAAAAGAGTTTG
124163 AAAAAGAGTTTG
1 AAAAAGAGTTTG
124175 AAAAAGAG
1 AAAAAGAG
124183 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:132430 original size:21 final size:23
Alignment explanation
Indices: 132385--132431 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
132375 GTCACCTCAA
* *
132385 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
132408 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
132429 TAA
1 TAA
132432 TCATACTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:134202 original size:34 final size:34
Alignment explanation
Indices: 134163--134231 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
134153 ATACCTTCGC
134163 GATAAAGCATCTGCAACGATATTTTCCTTACCTT
1 GATAAAGCATCTGCAACGATATTTTCCTTACCTT
134197 GATAAAGCATCTGCAACGATATTTTCCTTACCTT
1 GATAAAGCATCTGCAACGATATTTTCCTTACCTT
134231 G
1 G
134232 CTTATACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (34 bp):
GATAAAGCATCTGCAACGATATTTTCCTTACCTT
Done.