Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013677.1 Kokia drynarioides strain JFW-HI SEQ_128705, 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: 390591
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 52 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37 TAATGGCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5411 original size:21 final size:21
Alignment explanation
Indices: 5366--5418 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5356 ATGCGAGAGT
* *
5366 TCTACCGATACAAGTGACTCT
1 TCTACCGATACAAGTGACACC
**
5387 TCTACCGATACAAGTTTCACC
1 TCTACCGATACAAGTGACACC
*
5408 TCTACTGATAC
1 TCTACCGATAC
5419 TAAAAACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (21 bp):
TCTACCGATACAAGTGACACC
Found at i:7826 original size:26 final size:27
Alignment explanation
Indices: 7772--7830 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 27
7762 TGTGAAGGAT
7772 ATTAATCTAAAGCATTAAACTAAACTAA
1 ATTAATCTAAAG-ATTAAACTAAACTAA
7800 ATTAATCT-AAG-TTAAAGCTAAACTAA
1 ATTAATCTAAAGATTAAA-CTAAACTAA
7826 ATTAA
1 ATTAA
7831 ATTCCTAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.17
26 14 0.47
27 3 0.10
28 8 0.27
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.31
Consensus pattern (27 bp):
ATTAATCTAAAGATTAAACTAAACTAA
Found at i:20218 original size:21 final size:22
Alignment explanation
Indices: 20189--20231 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
20179 AACTAAGTAT
*
20189 AAATAGGTTGATTAAGG-TTAA
1 AAATAGGTTAATTAAGGCTTAA
*
20210 AAATGGGTTAATTAAGGCTTAA
1 AAATAGGTTAATTAAGGCTTAA
20232 TGATGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (22 bp):
AAATAGGTTAATTAAGGCTTAA
Found at i:28502 original size:20 final size:20
Alignment explanation
Indices: 28466--28515 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
28456 TCATTAAGAT
*
28466 TTAATTAACCACTTTTA-ATC
1 TTAATTAAACACTTTTATA-C
28486 TTAATTAAAC-CTATTTATAC
1 TTAATTAAACACT-TTTATAC
28506 TTAATATAAA
1 TTAAT-TAAA
28516 TCATACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAAACACTTTTATAC
Found at i:29160 original size:15 final size:13
Alignment explanation
Indices: 29131--29155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29121 TGAATAACAA
29131 TATATAAAACTTG
1 TATATAAAACTTG
29144 TATATAAAACTT
1 TATATAAAACTT
29156 ATGTAAATAT
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:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
TATATAAAACTTG
Found at i:34131 original size:34 final size:34
Alignment explanation
Indices: 34088--34174 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 34
34078 TACACAGTTA
* ** *
34088 ACCATCCAACACACCAGATGCTTGTATGAGCCAT
1 ACCAACCAACACACCAGATGCTCATATGAGCCAG
* *
34122 ACCAACCAACACACAAAATGCTCATATGAGCCAG
1 ACCAACCAACACACCAGATGCTCATATGAGCCAG
*
34156 ACCAACCAGCACACCAGAT
1 ACCAACCAACACACCAGAT
34175 AACACTATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.39, C:0.34, G:0.13, T:0.14
Consensus pattern (34 bp):
ACCAACCAACACACCAGATGCTCATATGAGCCAG
Found at i:36014 original size:2 final size:2
Alignment explanation
Indices: 36007--36078 Score: 117
Period size: 2 Copynumber: 36.0 Consensus size: 2
35997 TGAAATTATA
*
36007 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
36049 TG TG TG TG TG TG TG TG CG CG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36079 AATTGGTACA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.01, C:0.03, G:0.49, T:0.47
Consensus pattern (2 bp):
TG
Found at i:36783 original size:18 final size:17
Alignment explanation
Indices: 36748--36786 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
36738 ATATTTTAAT
*
36748 ATTT-CTATATCCAATG
1 ATTTACTATATCAAATG
36764 ATTTACTATGATCAAATG
1 ATTTACTAT-ATCAAATG
36782 ATTTA
1 ATTTA
36787 TTTCCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 4 0.20
18 12 0.60
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTTACTATATCAAATG
Found at i:36913 original size:57 final size:57
Alignment explanation
Indices: 36844--36969 Score: 180
Period size: 57 Copynumber: 2.2 Consensus size: 57
36834 TTAGGTCATA
* ** * *
36844 TTCATTTTTCATTTTTATTTTGCCGAAAACCATATTCATTTCCAAATTATTCCATTTC
1 TTCA-TTTTCATTTTCATTTTGAAGAAAACCATAATCATTTCCAAATGATTCCATTTC
*
36902 TTCATTTTCATTTTCATTTTGAAGAATACCATAATCATTTCCAAATGATTCCATTTC
1 TTCATTTTCATTTTCATTTTGAAGAAAACCATAATCATTTCCAAATGATTCCATTTC
*
36959 TGCATTTTCAT
1 TTCATTTTCAT
36970 ATTCTCACCC
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
57 57 0.93
58 4 0.07
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (57 bp):
TTCATTTTCATTTTCATTTTGAAGAAAACCATAATCATTTCCAAATGATTCCATTTC
Found at i:38492 original size:3 final size:3
Alignment explanation
Indices: 38459--38530 Score: 92
Period size: 3 Copynumber: 24.3 Consensus size: 3
38449 CTTAGACTAC
* * * * *
38459 AAT AAC AAT AAC AAC AAT AAC AAT AA- CAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38506 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
38531 GTCTAGCACG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
2 1 0.02
3 59 0.98
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:51357 original size:22 final size:24
Alignment explanation
Indices: 51314--51357 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
51304 CTTTATTTGA
51314 TTTTGATATATCAAATTAAAATGT
1 TTTTGATATATCAAATTAAAATGT
*
51338 TTTTGA-ATAT-AAGTTAAAAT
1 TTTTGATATATCAAATTAAAAT
51358 TGACAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (24 bp):
TTTTGATATATCAAATTAAAATGT
Found at i:52827 original size:10 final size:10
Alignment explanation
Indices: 52814--52838 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52804 AAAGCTACTT
52814 AAAGTAAATC
1 AAAGTAAATC
52824 AAAGTAAATC
1 AAAGTAAATC
52834 AAAGT
1 AAAGT
52839 GTTGTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (10 bp):
AAAGTAAATC
Found at i:54967 original size:17 final size:18
Alignment explanation
Indices: 54941--54974 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54931 CAACTAAAGT
*
54941 AAAAAGAAATGTAATGAC
1 AAAAAGAAATGCAATGAC
54959 AAAAA-AAATGCAATGA
1 AAAAAGAAATGCAATGA
54975 TAGTAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (18 bp):
AAAAAGAAATGCAATGAC
Found at i:57327 original size:15 final size:15
Alignment explanation
Indices: 57302--57340 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
57292 TCCTGCAAAT
* *
57302 AAATTAAAGTGAAAC
1 AAATAAAAGTGAAAA
*
57317 AAGTAAAAGTGAAAA
1 AAATAAAAGTGAAAA
57332 AAATAAAAG
1 AAATAAAAG
57341 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.03, G:0.15, T:0.15
Consensus pattern (15 bp):
AAATAAAAGTGAAAA
Found at i:68588 original size:13 final size:14
Alignment explanation
Indices: 68572--68629 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 14
68562 TAGGAAACAT
68572 TTTTCTTCTTTT-C
1 TTTTCTTCTTTTAC
68585 TTTTC-TCTTTTAC
1 TTTTCTTCTTTTAC
*
68598 TTTT-TTC-TTTCC
1 TTTTCTTCTTTTAC
*
68610 TTTTC-TCATTTTCC
1 TTTTCTTC-TTTTAC
68624 TTTTCT
1 TTTTCT
68630 AAGTGACTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 16 0.42
13 12 0.32
14 10 0.26
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTTCTTTTAC
Found at i:68612 original size:25 final size:27
Alignment explanation
Indices: 68572--68629 Score: 84
Period size: 25 Copynumber: 2.2 Consensus size: 27
68562 TAGGAAACAT
*
68572 TTTTCTTCTTTTCTTTTCTC-TTTTAC
1 TTTTCTTCTTTCCTTTTCTCATTTTAC
*
68598 TTTT-TTCTTTCCTTTTCTCATTTTCC
1 TTTTCTTCTTTCCTTTTCTCATTTTAC
68624 TTTTCT
1 TTTTCT
68630 AAGTGACTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 14 0.50
26 13 0.46
27 1 0.04
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTCTTCTTTCCTTTTCTCATTTTAC
Found at i:74468 original size:30 final size:30
Alignment explanation
Indices: 74433--74503 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
74423 TCAGATCCTT
* *
74433 TCTTCAAAACTAGATTTTTGTCCATGCATC
1 TCTTCAAAACTAGACTTGTGTCCATGCATC
*
74463 TCTTCAAAACTAGACTTGTGTCCTTGCATC
1 TCTTCAAAACTAGACTTGTGTCCATGCATC
74493 TCTTCAAAACT
1 TCTTCAAAACT
74504 CTTGCCAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (30 bp):
TCTTCAAAACTAGACTTGTGTCCATGCATC
Found at i:91317 original size:15 final size:15
Alignment explanation
Indices: 91297--91333 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
91287 TTGCAGCATG
91297 AGTGCTCGCAACACC
1 AGTGCTCGCAACACC
*
91312 AGTGCTCGCAACACT
1 AGTGCTCGCAACACC
91327 AGTGCTC
1 AGTGCTC
91334 ACATCTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.35, G:0.22, T:0.19
Consensus pattern (15 bp):
AGTGCTCGCAACACC
Found at i:95310 original size:29 final size:28
Alignment explanation
Indices: 95240--95312 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
95230 CGAATACAAT
*
95240 TAATAATACAATAAAAATATAATTATAG
1 TAATAATACAATAAAAATATAATCATAG
* * *
95268 TATTAAATAAAATAACAATATAATCATAG
1 TAAT-AATACAATAAAAATATAATCATAG
95297 TAATAATGACAATAAA
1 TAATAAT-ACAATAAA
95313 TATTAATTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 6 0.17
29 30 0.83
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.30
Consensus pattern (28 bp):
TAATAATACAATAAAAATATAATCATAG
Found at i:95571 original size:4 final size:4
Alignment explanation
Indices: 95562--95698 Score: 55
Period size: 4 Copynumber: 31.8 Consensus size: 4
95552 AACTTTAATG
** * * *
95562 ATAA ATAA ATAA ATAA CCAA ATAA GA-GA ATAACA ATAA ATGA A-AA TTAA
1 ATAA ATAA ATAA ATAA ATAA ATAA -ATAA AT-A-A ATAA ATAA ATAA ATAA
* * *
95611 ATAA AAATA ATAAA ATAA ATAACA ATAAA ATGAC ATGAA AATAA ATAA ACAAA
1 ATAA ATA-A AT-AA ATAA AT-A-A AT-AA AT-AA AT-AA -ATAA ATAA A-TAA
*
95664 ATAA ATAA ATAA ACAA A-AA ATAA ATAA ATTAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A-TAA ATA
95699 CCAAAATAAA
Statistics
Matches: 102, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
3 5 0.05
4 61 0.60
5 25 0.25
6 11 0.11
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:95615 original size:15 final size:14
Alignment explanation
Indices: 95595--95698 Score: 72
Period size: 15 Copynumber: 7.3 Consensus size: 14
95585 AGAGAATAAC
95595 AATAAATGAAAATTA
1 AATAAAT-AAAATTA
*
95610 AATAAA-AATAATAA
1 AATAAATAA-AATTA
*
95624 AATAAATAACAATAA
1 AATAAATAA-AATTA
*
95639 AATGACATGAAAA-TA
1 AAT-AAAT-AAAATTA
*
95654 AATAAACAAAA-TA
1 AATAAATAAAATTA
**
95667 AATAAATAAACAAAA
1 AATAAATAAA-ATTA
95682 AATAAAT-AAATTA
1 AATAAATAAAATTA
95695 AATA
1 AATA
95699 CCAAAATAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
13 23 0.32
14 15 0.21
15 28 0.38
16 5 0.07
17 2 0.03
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAATAAAATTA
Found at i:95631 original size:18 final size:20
Alignment explanation
Indices: 95589--95638 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
95579 CAAATAAGAG
95589 AATAACAATAAATGAAAATTA
1 AATAACAAT-AATGAAAATTA
*
95610 AATAAAAATAAT-AAAA-TA
1 AATAACAATAATGAAAATTA
95628 AATAACAATAA
1 AATAACAATAA
95639 AATGACATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 12 0.44
19 4 0.15
20 3 0.11
21 8 0.30
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (20 bp):
AATAACAATAATGAAAATTA
Found at i:95667 original size:44 final size:43
Alignment explanation
Indices: 95595--95708 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 43
95585 AGAGAATAAC
95595 AATAAATGAAAATTAAATAAA-AATAATAAAATAAAT-AACAATAA
1 AATAAATGAAAA-TAAATAAACAA-AATAAAATAAATAAACAA-AA
*
95639 AATGACATGAAAATAAATAAACAAAAT-AAATAAATAAACAAAA
1 AAT-AAATGAAAATAAATAAACAAAATAAAATAAATAAACAAAA
* *
95682 AATAAAT-AAATTAAAT-ACCAAAATAAA
1 AATAAATGAAAATAAATAAACAAAATAAA
95709 TACCAAAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
40 7 0.11
41 10 0.16
42 3 0.05
43 13 0.21
44 19 0.31
45 10 0.16
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (43 bp):
AATAAATGAAAATAAATAAACAAAATAAAATAAATAAACAAAA
Found at i:95671 original size:17 final size:15
Alignment explanation
Indices: 95648--95691 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 15
95638 AAATGACATG
95648 AAAATAAATAAACAAA
1 AAAATAAATAAAC-AA
95664 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
95680 AAAATAAATAAA
1 AAAATAAATAAA
95692 TTAAATACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.41
16 4 0.15
17 12 0.44
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:95710 original size:4 final size:4
Alignment explanation
Indices: 95649--95698 Score: 57
Period size: 4 Copynumber: 12.2 Consensus size: 4
95639 AATGACATGA
* *
95649 AAAT AAAT AAACA AAAT AAAT AAAT AAAC AAA- AAAT AAAT AAATT AAAT
1 AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT
95698 A
1 A
95699 CCAAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
3 3 0.08
4 30 0.75
5 7 0.17
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:96011 original size:24 final size:24
Alignment explanation
Indices: 95984--96034 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
95974 CAAAAGAAGT
95984 TCCTCTCTGAACAAATAAAAAAAA
1 TCCTCTCTGAACAAATAAAAAAAA
*
96008 TCCTCTCTTAACAAATAAAAAAAA
1 TCCTCTCTGAACAAATAAAAAAAA
96032 TCC
1 TCC
96035 CCCTCTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.24
Consensus pattern (24 bp):
TCCTCTCTGAACAAATAAAAAAAA
Found at i:96040 original size:25 final size:24
Alignment explanation
Indices: 95988--96041 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
95978 AGAAGTTCCT
* *
95988 CTCTGAACAAATAAAAAAAATCCT
1 CTCTTAACAAATAAAAAAAATCCC
96012 CTCTTAACAAATAAAAAAAATCCCC
1 CTCTTAACAAATAAAAAAAAT-CCC
96037 CTCTT
1 CTCTT
96042 TACATTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (24 bp):
CTCTTAACAAATAAAAAAAATCCC
Found at i:96782 original size:45 final size:45
Alignment explanation
Indices: 96635--97077 Score: 481
Period size: 45 Copynumber: 9.6 Consensus size: 45
96625 TTCAATTTGT
* * *
96635 CCCTCTGGATTAGGGGTAATAGATTGGATTTGGTATTGTGACTTCAATCTGC
1 CCCTCTAGATTAGGGGTAAAAGATTGGA--TGG---TG-G-CTTCAATCTAC
* *
96687 CCCTCTAGATTAGGGGTAAAAGATTAGATTTGGTGACTTCAATCTAC
1 CCCTCTAGATTAGGGGTAAAAGATTGGA--TGGTGGCTTCAATCTAC
* * *
96734 CCCTCTAGATTAGGAGTAAAAGACTGGATGGTGGCTTCAATCTGC
1 CCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTAC
* *
96779 CCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTAT
1 CCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTAC
* *
96824 CCCTCAAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGC
1 CCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTAC
* * * * * * *
96869 CCCTTTGGATTACGGGTAAAAGACTAGATGGTGGCTTTAATCTAT
1 CCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTAC
* * *
96914 CCCTCTAGATTAGGGGTAAAAGATTGAATGTGGTGACTTCAATCTGC
1 CCCTCTAGATTAGGGGTAAAAGATTGGA--TGGTGGCTTCAATCTAC
* ** *
96961 CCCTCTAGATTATGGGTAAAAGACCGGATGATGGCTTCAATCTAC
1 CCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTAC
* * *
97006 CCCTCTGGATTAGGGGTAAAATATTGGATATGGTGACTTCAATCTAC
1 CCCTCTAGATTAGGGGTAAAAGATTGG--ATGGTGGCTTCAATCTAC
** *
97053 CCAACTGGATTAGGGGTAAAAGATT
1 CCCTCTAGATTAGGGGTAAAAGATT
97078 ATATTGTGGC
Statistics
Matches: 332, Mismatches: 55, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
45 190 0.57
47 110 0.33
49 2 0.01
52 30 0.09
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (45 bp):
CCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTAC
Found at i:96845 original size:90 final size:90
Alignment explanation
Indices: 96672--97089 Score: 521
Period size: 92 Copynumber: 4.6 Consensus size: 90
96662 ATTTGGTATT
*
96672 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTAGATTTGGTGACTTCAATCTACCCC
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTAGA--TGGTGGCTTCAATCTACCCC
* *
96737 TCTAGATTAGGAGTAAAAGACTGGATG
64 TCTAGATTAGGGGTAAAAGATTGGATG
* * * *
96764 GTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTATCCCTC
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTACCCCTC
*
96829 AAGATTAGGGGTAAAAGATTGGATG
66 TAGATTAGGGGTAAAAGATTGGATG
* * * * * * *
96854 GTGGCTTCAATCTGCCCCTTTGGATTACGGGTAAAAGACTAGATGGTGGCTTTAATCTATCCCTC
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTACCCCTC
*
96919 TAGATTAGGGGTAAAAGATTGAATGTG
66 TAGATTAGGGGTAAAAGATTGGA--TG
* *** *
96946 GTGACTTCAATCTGCCCCTCTAGATTATGGGTAAAAGACCGGATGATGGCTTCAATCTACCCCTC
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTACCCCTC
* *
97011 TGGATTAGGGGTAAAATATTGGATATG
66 TAGATTAGGGGTAAAAGATTGG--ATG
* ** * * *
97038 GTGACTTCAATCTACCCAACTGGATTAGGGGTAAAAGATTATATTGTGGCTT
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTAGATGGTGGCTT
97090 TAATATGTCC
Statistics
Matches: 283, Mismatches: 39, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
90 122 0.43
92 160 0.57
94 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (90 bp):
GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTACCCCTC
TAGATTAGGGGTAAAAGATTGGATG
Found at i:97307 original size:49 final size:49
Alignment explanation
Indices: 97254--97649 Score: 319
Period size: 49 Copynumber: 8.1 Consensus size: 49
97244 TTAAATCTGT
* * * * *
97254 TCCCTCTTTAATTTTAGGGTGTTAGATCCGTCATTGTGGCTTCAATCTA
1 TCCCTCTTCAATTTTAAGGTGTTAGATCCATCGTTATGGCTTCAATCTA
* * * * * *
97303 TCCCTTTTCGATTTTAGGGTGTTATG-TCCACCGTTACGGCTTCAACCTA
1 TCCCTCTTCAATTTTAAGGTGTTA-GATCCATCGTTATGGCTTCAATCTA
* * * * ** *
97352 TCCCT-TTCAGTTTTAAGGTGTAAGATTCACCGTTACAGCTTCAATCTT
1 TCCCTCTTCAATTTTAAGGTGTTAGATCCATCGTTATGGCTTCAATCTA
* * * *
97400 TCACTCTTCAATTTTAAGGTGTTAGGTCCGTCGTTATGGCTTCAACCTA
1 TCCCTCTTCAATTTTAAGGTGTTAGATCCATCGTTATGGCTTCAATCTA
* * * * * * *
97449 TCCCTCTTCAATTTTAAGGTGTAAGATCTATCATTGTGACTTCAATATT
1 TCCCTCTTCAATTTTAAGGTGTTAGATCCATCGTTATGGCTTCAATCTA
* * * * * * *
97498 TCCCTCTTCAATTATAGGGTGTTAGGTCCATCATTATGACGTCAACCTA
1 TCCCTCTTCAATTTTAAGGTGTTAGATCCATCGTTATGGCTTCAATCTA
* * ** * *
97547 TCCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTACGGCTGAAATATT
1 TCCCTCTTCAATTTTAAGGTGTTAGATCCATCGTTATGGCTTCAATCTA
* * * * ** * *
97596 TCCCTCTTCCATTTTAGGGTGTTAGGTCCACCGTTGCGGCTTTAACCTA
1 TCCCTCTTCAATTTTAAGGTGTTAGATCCATCGTTATGGCTTCAATCTA
97645 TCCCT
1 TCCCT
97650 TTCCAACTAT
Statistics
Matches: 271, Mismatches: 73, Indels: 6
0.77 0.21 0.02
Matches are distributed among these distances:
47 1 0.00
48 37 0.14
49 232 0.86
50 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (49 bp):
TCCCTCTTCAATTTTAAGGTGTTAGATCCATCGTTATGGCTTCAATCTA
Found at i:97502 original size:146 final size:148
Alignment explanation
Indices: 97222--97507 Score: 335
Period size: 146 Copynumber: 1.9 Consensus size: 148
97212 TTTTTAAAAT
** * * *
97222 GTGTAAGATTCGTCGTTACAGCTTAAATCTGTTCCCTCTTTAATTTTAGGGTGTTAGATCCGTCA
1 GTGTAAGATTCACCGTTACAGCTTAAATCTGTTCACTCTTCAATTTTAAGGTGTTAGATCCGTCA
* * * * * * * * *
97287 TTGTGGCTTCAATCTATCCCTTTTCGATTTTAGGGTGTTATGTCCACCGTTACGGCTTCAACCTA
66 TTATGGCTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAAGTCCACCATTACGACTTCAACATA
97352 TCCCT-TTCAGTTTTAAG
131 TCCCTCTTCAGTTTTAAG
* * *
97369 GTGTAAGATTCACCGTTACAGCTTCAATCT-TTCACTCTTCAATTTTAAGGTGTTAGGTCCGTCG
1 GTGTAAGATTCACCGTTACAGCTTAAATCTGTTCACTCTTCAATTTTAAGGTGTTAGATCCGTCA
* * ** *
97433 TTATGGCTTCAACCTATCCCTCTTCAATTTTAAGGTG-TAAGATCTATCATTGTGACTTCAATAT
66 TTATGGCTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAAG-TCCACCATTACGACTTCAACAT
*
97497 TTCCCTCTTCA
130 ATCCCTCTTCA
97508 ATTATAGGGT
Statistics
Matches: 114, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
145 3 0.03
146 80 0.70
147 31 0.27
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.40
Consensus pattern (148 bp):
GTGTAAGATTCACCGTTACAGCTTAAATCTGTTCACTCTTCAATTTTAAGGTGTTAGATCCGTCA
TTATGGCTTCAACCTATCCCTCTTCAATTTTAAGGTGTTAAGTCCACCATTACGACTTCAACATA
TCCCTCTTCAGTTTTAAG
Found at i:97519 original size:98 final size:98
Alignment explanation
Indices: 97254--97649 Score: 427
Period size: 98 Copynumber: 4.1 Consensus size: 98
97244 TTAAATCTGT
* * * * * * * * *
97254 TCCCTCTTTAATTTTAGGGTGTTAGATCCGTCATTGTGGCTTCAATCTATCCCTTTTCGATTTTA
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCATCATTGTGACTTCAATATTTCCCTCTTCAATTTTA
*
97319 GGGTGTTATGTCCACCGTTACGGCTTCAACCTA
66 GGGTGTTAGGTCCACCGTTACGGCTTCAACCTA
* * * * ** * *
97352 TCCCT-TTCAGTTTTAAGGTGTAAGATTCACCGTT-ACAGCTTCAATCTTTCACTCTTCAATTTT
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCATCATTGTGA-CTTCAATATTTCCCTCTTCAATTTT
* ** *
97415 AAGGTGTTAGGTCCGTCGTTATGGCTTCAACCTA
65 AGGGTGTTAGGTCCACCGTTACGGCTTCAACCTA
* *
97449 TCCCTCTTCAATTTTAAGGTGTAAGATCTATCATTGTGACTTCAATATTTCCCTCTTCAATTATA
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCATCATTGTGACTTCAATATTTCCCTCTTCAATTTTA
* * * * *
97514 GGGTGTTAGGTCCATCATTATGACGTCAACCTA
66 GGGTGTTAGGTCCACCGTTACGGCTTCAACCTA
* ** * ** *
97547 TCCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTACGGCTGAAATATTTCCCTCTTCCATTTTA
1 TCCCTCTTCAATTTTAAGGTGTAAGATCCATCATTGTGACTTCAATATTTCCCTCTTCAATTTTA
* *
97612 GGGTGTTAGGTCCACCGTTGCGGCTTTAACCTA
66 GGGTGTTAGGTCCACCGTTACGGCTTCAACCTA
97645 TCCCT
1 TCCCT
97650 TTCCAACTAT
Statistics
Matches: 244, Mismatches: 51, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
97 76 0.31
98 167 0.68
99 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (98 bp):
TCCCTCTTCAATTTTAAGGTGTAAGATCCATCATTGTGACTTCAATATTTCCCTCTTCAATTTTA
GGGTGTTAGGTCCACCGTTACGGCTTCAACCTA
Found at i:107827 original size:26 final size:26
Alignment explanation
Indices: 107775--107827 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
107765 ATGCGACGAA
** * * *
107775 AATTCTGGATGTGCTCATGCAGTGAC
1 AATTCTGGACATGCTAATACAGCGAC
107801 AATTCTGGACATGCTAATACAGCGAC
1 AATTCTGGACATGCTAATACAGCGAC
107827 A
1 A
107828 TTAGTAGTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (26 bp):
AATTCTGGACATGCTAATACAGCGAC
Found at i:108863 original size:17 final size:17
Alignment explanation
Indices: 108832--108891 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
108822 CTAAAATACC
*
108832 ATGACAAATGGAAATGTA
1 ATGAC-AATGAAAATGTA
* *
108850 ATGACAATGCAAATGCA
1 ATGACAATGAAAATGTA
* * *
108867 ATGATAGTTAAAATGTA
1 ATGACAATGAAAATGTA
108884 ATGACAAT
1 ATGACAAT
108892 AGGAATGTGA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 28 0.85
18 5 0.15
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.25
Consensus pattern (17 bp):
ATGACAATGAAAATGTA
Found at i:114367 original size:17 final size:17
Alignment explanation
Indices: 114325--114359 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
114315 TATTTCTTTT
114325 TCTTCTTTTCTCTTTTCC
1 TCTT-TTTTCTCTTTTCC
114343 TCTTTTTTCTCTCTTTC
1 TCTTTTTTCTCT-TTTC
114360 GTTTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TCTTTTTTCTCTTTTCC
Found at i:122437 original size:32 final size:32
Alignment explanation
Indices: 122396--122459 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
122386 TTCAATACGT
122396 AGCTTAAAAACTGGAGTTGTTTTGTTGGCTAA
1 AGCTTAAAAACTGGAGTTGTTTTGTTGGCTAA
122428 AGCTTAAAAACTGGAGTTGTTTTGTTGGCTAA
1 AGCTTAAAAACTGGAGTTGTTTTGTTGGCTAA
122460 GTCTAAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (32 bp):
AGCTTAAAAACTGGAGTTGTTTTGTTGGCTAA
Found at i:123812 original size:20 final size:20
Alignment explanation
Indices: 123787--123826 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
123777 TTTAAGAATA
123787 AATAAATAGTACAACGAAGT
1 AATAAATAGTACAACGAAGT
123807 AATAAATAGTACAACGAAGT
1 AATAAATAGTACAACGAAGT
123827 TTACTATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.15, T:0.20
Consensus pattern (20 bp):
AATAAATAGTACAACGAAGT
Found at i:133093 original size:27 final size:27
Alignment explanation
Indices: 133039--133094 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
133029 GTGGTGGTAA
*
133039 ATCTTGTGGCAGCACTGGAGGAATATT
1 ATCTTGTGGCAGCACTGGAGGAAGATT
* * *
133066 ATCTTGTGGCAGCATTGGTGGTAGATT
1 ATCTTGTGGCAGCACTGGAGGAAGATT
133093 AT
1 AT
133095 TATTGTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.34
Consensus pattern (27 bp):
ATCTTGTGGCAGCACTGGAGGAAGATT
Found at i:135708 original size:21 final size:21
Alignment explanation
Indices: 135684--135723 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
135674 TTCTGCTATT
*
135684 TTGGATTGTAATTCCCTTGTC
1 TTGGATTATAATTCCCTTGTC
* *
135705 TTGGGTTATAATTGCCTTG
1 TTGGATTATAATTCCCTTG
135724 ATTAGACGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.47
Consensus pattern (21 bp):
TTGGATTATAATTCCCTTGTC
Found at i:136151 original size:21 final size:21
Alignment explanation
Indices: 136125--136193 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
136115 TAGTACAATT
* *
136125 TTCTACAGATACAAGTGTCAG
1 TTCTACAGATACAAGTCTCAC
* *
136146 TTCTACCGAAACAAGTCTCAC
1 TTCTACAGATACAAGTCTCAC
* *
136167 TTCTACTGATACAAGTCTTAC
1 TTCTACAGATACAAGTCTCAC
136188 TTCTAC
1 TTCTAC
136194 CGACACCAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (21 bp):
TTCTACAGATACAAGTCTCAC
Found at i:136956 original size:38 final size:35
Alignment explanation
Indices: 136866--136968 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 35
136856 TTGTTATTCA
* *
136866 TTTTACTCCCTGTTAATCCAAAGGTCATAATGCTCG
1 TTTTACTCCCTGTTGA-CCAAAGGTCATGATGCTCG
* * *
136902 TTTTACTCTCTATTGACACAAAGGTCATGATGCTTG
1 TTTTACTCCCTGTTGAC-CAAAGGTCATGATGCTCG
136938 TTTTTTACTCCCTGTTGACCCAAAGGTCATG
1 --TTTTACTCCCTGTTGA-CCAAAGGTCATG
136969 CCTGTTACCA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 1 0.02
36 29 0.52
38 25 0.45
39 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (35 bp):
TTTTACTCCCTGTTGACCAAAGGTCATGATGCTCG
Found at i:142651 original size:21 final size:21
Alignment explanation
Indices: 142634--142674 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
142624 GAGTTTTATC
142634 GAAACAAGTCTTACTTTTACT
1 GAAACAAGTCTTACTTTTACT
*
142655 GATACAAGTCTTACTTTTAC
1 GAAACAAGTCTTACTTTTAC
142675 CGACACCAAA
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:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (21 bp):
GAAACAAGTCTTACTTTTACT
Found at i:143363 original size:36 final size:36
Alignment explanation
Indices: 143267--143367 Score: 141
Period size: 35 Copynumber: 2.8 Consensus size: 36
143257 GTTCGTTATT
* * *
143267 CGTTTTACCCCCTGTTGACCCAAAGGTCATAATGCT
1 CGTTTTACTCCCTATTGACCCAAAGGTCATAATGCA
**
143303 CGTTTTA-TCTTTATTGACCCAAAGGTCATAATGCA
1 CGTTTTACTCCCTATTGACCCAAAGGTCATAATGCA
*
143338 CGTTTTACTCCCTATTGACCTAAAGGTCAT
1 CGTTTTACTCCCTATTGACCCAAAGGTCAT
143368 GCCTGTTACC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 30 0.54
36 26 0.46
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.35
Consensus pattern (36 bp):
CGTTTTACTCCCTATTGACCCAAAGGTCATAATGCA
Found at i:151841 original size:12 final size:12
Alignment explanation
Indices: 151824--151848 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
151814 TTGTCCCCTA
151824 GTCTGTTTACCC
1 GTCTGTTTACCC
151836 GTCTGTTTACCC
1 GTCTGTTTACCC
151848 G
1 G
151849 CGGCTTCAGT
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:0.08, C:0.32, G:0.20, T:0.40
Consensus pattern (12 bp):
GTCTGTTTACCC
Found at i:160244 original size:51 final size:51
Alignment explanation
Indices: 160159--160263 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
160149 CGCCTAGTTG
* *
160159 CAAAGTCACTCGGGTATTTTTGAGATCTCTGCTCTCAAGTTTCTCAAACAC
1 CAAAATCACTCGGGTATTTTTGAGATCTCCGCTCTCAAGTTTCTCAAACAC
*
160210 CAAAATCACTTGGGTATTTTTGAGATCTCCGCTCTCAAGTTTCTCAAACAC
1 CAAAATCACTCGGGTATTTTTGAGATCTCCGCTCTCAAGTTTCTCAAACAC
160261 CAA
1 CAA
160264 TAGAGGTATC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (51 bp):
CAAAATCACTCGGGTATTTTTGAGATCTCCGCTCTCAAGTTTCTCAAACAC
Found at i:168774 original size:16 final size:16
Alignment explanation
Indices: 168753--168788 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
168743 AAATAATACC
*
168753 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
*
168769 AAAATTAAAAGTTTCA
1 AAAATTAAAAGTCTCA
168785 AAAA
1 AAAA
168789 CACTTTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:169290 original size:17 final size:18
Alignment explanation
Indices: 169257--169290 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
169247 TTTGGTGAAT
169257 CTACTTCCTTATACAAAC
1 CTACTTCCTTATACAAAC
*
169275 CTACTTTCTT-TACAAA
1 CTACTTCCTTATACAAA
169291 ATTACAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (18 bp):
CTACTTCCTTATACAAAC
Found at i:176320 original size:24 final size:24
Alignment explanation
Indices: 176267--176320 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
176257 ACCCGTTTTA
*
176267 AATTTATAATACTTTATATTATAT
1 AATTTATAATACTATATATTATAT
**
176291 TTTTTATATATA-TATATATTATAT
1 AATTTATA-ATACTATATATTATAT
176315 AATTTA
1 AATTTA
176321 AAACACTTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTTATAATACTATATATTATAT
Found at i:176407 original size:14 final size:12
Alignment explanation
Indices: 176373--176470 Score: 51
Period size: 11 Copynumber: 7.6 Consensus size: 12
176363 CTCTAATATA
176373 AATAT-TAAAAT
1 AATATATAAAAT
176384 AATAT-TAAAAT
1 AATATATAAAAT
176395 AACTATATAAAAAATT
1 AA-TATAT--AAAA-T
*
176411 CAATAAATAAAA-
1 -AATATATAAAAT
176423 AATATATAAAATT
1 AATATATAAAA-T
*
176436 ATTAAATATTAAAAT
1 A--ATATA-TAAAAT
176451 AATATAATATAAAT
1 AATAT-ATA-AAAT
176465 -ATATAT
1 AATATAT
176471 TTTAAAAATT
Statistics
Matches: 70, Mismatches: 4, Indels: 25
0.71 0.04 0.25
Matches are distributed among these distances:
11 23 0.33
12 5 0.07
13 11 0.16
14 9 0.13
15 10 0.14
16 10 0.14
17 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (12 bp):
AATATATAAAAT
Found at i:176415 original size:28 final size:28
Alignment explanation
Indices: 176384--176465 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
176374 ATATTAAAAT
*
176384 AATATTAAAATAACTATATAAAA-AATTC
1 AATATTAAAATAA-TATATAAAATAATTA
* *
176412 AATAAATAAAA-AATATATAAAATTATTA
1 AAT-ATTAAAATAATATATAAAATAATTA
176440 AATATTAAAATAATATAATATAAATA
1 AATATTAAAATAATAT-ATA-AAATA
176466 TATATTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 15 0.34
28 16 0.36
29 9 0.20
30 4 0.09
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
AATATTAAAATAATATATAAAATAATTA
Found at i:176449 original size:25 final size:25
Alignment explanation
Indices: 176399--176457 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
176389 TAAAATAACT
*
176399 ATATAAAAAATTCAATAAATAAAAA
1 ATATATAAAATTCAATAAATAAAAA
* *
176424 ATATATAAAATT-ATTAAATATTAAA
1 ATATATAAAATTCAATAAATA-AAAA
176449 ATAATATAA
1 AT-ATATAA
176458 TATAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 7 0.24
25 16 0.55
26 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
ATATATAAAATTCAATAAATAAAAA
Found at i:200472 original size:53 final size:52
Alignment explanation
Indices: 200383--200498 Score: 121
Period size: 53 Copynumber: 2.2 Consensus size: 52
200373 AAATAAATTC
* *
200383 AAAAAG-AAAAGTTTTAGGGTTTAAAAGG-AAGTAAAAATTTTGAGGAAAAGT
1 AAAAAGAAAAAGTTTTAGGGTTTAAAAGGAAAG-AAAAAATTTAAGGAAAAGT
* * **
200434 AAAATAGAAAAAGTTTTGGGGTTTAGAGAAGTAAA-AAAAAATTTAAGGATGAGT
1 AAAA-AGAAAAAGTTTTAGGGTTTA-A-AAGGAAAGAAAAAATTTAAGGAAAAGT
200488 AAAAAGAAAAA
1 AAAAAGAAAAA
200499 AAATTTGGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
51 4 0.07
52 2 0.04
53 23 0.43
54 20 0.37
55 3 0.06
56 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.23
Consensus pattern (52 bp):
AAAAAGAAAAAGTTTTAGGGTTTAAAAGGAAAGAAAAAATTTAAGGAAAAGT
Found at i:205176 original size:18 final size:18
Alignment explanation
Indices: 205145--205179 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
205135 ATTACATGTG
**
205145 ATAAAAATTTATAAAAAA
1 ATAAAAATCAATAAAAAA
205163 ATAAAAATCAATAAAAA
1 ATAAAAATCAATAAAAA
205180 GTTATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAAATCAATAAAAAA
Found at i:205188 original size:9 final size:9
Alignment explanation
Indices: 205145--205297 Score: 80
Period size: 10 Copynumber: 16.3 Consensus size: 9
205135 ATTACATGTG
205145 ATAAAAATTT
1 ATAAAAA-TT
*
205155 ATAAAAA-A
1 ATAAAAATT
*
205163 ATAAAAATCA
1 ATAAAAAT-T
205173 ATAAAAAGTT
1 ATAAAAA-TT
205183 ATAAAAATT
1 ATAAAAATT
**
205192 ATTAAATTTT
1 A-TAAAAATT
205202 AATAAAAA-T
1 -ATAAAAATT
*
205211 ATAAAATTT
1 ATAAAAATT
205220 ATTTAAAAAATT
1 A--T-AAAAATT
*
205232 AGAAAAATT
1 ATAAAAATT
*
205241 ATAAAAATC
1 ATAAAAATT
* *
205250 GTAAAAAAT
1 ATAAAAATT
205259 A-AAAAATGT
1 ATAAAAAT-T
**
205268 A-AAATTTT
1 ATAAAAATT
*
205276 ATAAAAATC
1 ATAAAAATT
205285 ATAAAAAATT
1 AT-AAAAATT
205295 ATA
1 ATA
205298 CACCGCATCA
Statistics
Matches: 109, Mismatches: 22, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
8 20 0.18
9 39 0.36
10 40 0.37
11 3 0.03
12 7 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:205237 original size:21 final size:22
Alignment explanation
Indices: 205199--205242 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
205189 ATTATTAAAT
* *
205199 TTTAATAAAAATATAAAATTTA
1 TTTAATAAAAATAGAAAAATTA
*
205221 TTTAA-AAAATTAGAAAAATTA
1 TTTAATAAAAATAGAAAAATTA
205242 T
1 T
205243 AAAAATCGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTAATAAAAATAGAAAAATTA
Found at i:205256 original size:19 final size:19
Alignment explanation
Indices: 205234--205297 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
205224 AAAAAATTAG
205234 AAAAATTATAAAAATCGTA
1 AAAAATTATAAAAATCGTA
205253 AAAAA-TA-AAAAAT-GTA
1 AAAAATTATAAAAATCGTA
** *
205269 AAATTTTATAAAAATCATA
1 AAAAATTATAAAAATCGTA
205288 AAAAATTATA
1 AAAAATTATA
205298 CACCGCATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
16 6 0.16
17 8 0.22
18 8 0.22
19 15 0.41
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAAATTATAAAAATCGTA
Found at i:205269 original size:16 final size:17
Alignment explanation
Indices: 205222--205295 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 17
205212 TAAAATTTAT
205222 TTAAAAAAT-TAGAAAAA
1 TTAAAAAATGTA-AAAAA
205239 TTATAAAAATCGTAAAAAA
1 TTA-AAAAAT-GTAAAAAA
**
205258 -TAAAAAATGTAAAATT
1 TTAAAAAATGTAAAAAA
*
205274 TTATAAAAATCATAAAAAA
1 TTA-AAAAAT-GTAAAAAA
205293 TTA
1 TTA
205296 TACACCGCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
16 6 0.13
17 11 0.24
18 14 0.30
19 13 0.28
20 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (17 bp):
TTAAAAAATGTAAAAAA
Found at i:205335 original size:13 final size:13
Alignment explanation
Indices: 205317--205341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
205307 AAAAAGACCC
205317 TTTAACCATTAAG
1 TTTAACCATTAAG
205330 TTTAACCATTAA
1 TTTAACCATTAA
205342 CAGTTAAAGT
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:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTAACCATTAAG
Found at i:205518 original size:19 final size:21
Alignment explanation
Indices: 205496--205540 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
205486 TTTTTATTTT
205496 TTACGAA-TTTTAT-ATTTCC
1 TTACGAATTTTTATAATTTCC
*
205515 TTAC-AATTTTTATAATTTTC
1 TTACGAATTTTTATAATTTCC
205535 TTACGA
1 TTACGA
205541 CTTTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.09
19 10 0.45
20 9 0.41
21 1 0.05
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.53
Consensus pattern (21 bp):
TTACGAATTTTTATAATTTCC
Found at i:205580 original size:9 final size:9
Alignment explanation
Indices: 205551--205720 Score: 55
Period size: 9 Copynumber: 18.4 Consensus size: 9
205541 CTTTATAAAA
205551 TTTTAT-AT
1 TTTTATAAT
*
205559 TTTTCT-AT
1 TTTTATAAT
205567 ATTTTATAATT
1 -TTTTATAA-T
* *
205578 TTTTTTACGT
1 TTTTATA-AT
*
205588 TTTTATAAAA
1 TTTTAT-AAT
*
205598 TTTTATAAA
1 TTTTATAAT
*
205607 ATTT-TAAT
1 TTTTATAAT
*
205615 TTTTTTAATTT
1 TTTTATAA--T
*
205626 TTTTATGAT
1 TTTTATAAT
205635 TTTTAT-AT
1 TTTTATAAT
*
205643 GTTTTA-AGT
1 -TTTTATAAT
205652 ATTTTAT-AT
1 -TTTTATAAT
*
205661 TTTTATTAAAA
1 TTTTA-T-AAT
*
205672 TTTAATAAT
1 TTTTATAAT
*
205681 TTTTATAAC
1 TTTTATAAT
**
205690 TTTTATTGT
1 TTTTATAAT
* *
205699 TTTTTTATT
1 TTTTATAAT
*
205708 TTTTATTAT
1 TTTTATAAT
205717 TTTT
1 TTTT
205721 GTCATATGTT
Statistics
Matches: 119, Mismatches: 29, Indels: 27
0.68 0.17 0.15
Matches are distributed among these distances:
8 20 0.17
9 65 0.55
10 20 0.17
11 14 0.12
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTTATAAT
Found at i:205638 original size:47 final size:46
Alignment explanation
Indices: 205518--205641 Score: 137
Period size: 47 Copynumber: 2.7 Consensus size: 46
205508 TATTTCCTTA
* * *
205518 CAATTTTTATAATTTTCTTACGA-CTTTATAAAATTTTATATTTTT
1 CAATTTTTATAATTTTTTTACGATTTTTATAAAATTTTATAATTTT
*
205563 CTATATTTTATAATTTTTTTTACG-TTTTTATAAAATTTTATAAAATTTT
1 CAAT-TTTTATAA-TTTTTTTACGATTTTTATAAAATTTTAT--AATTTT
* *
205612 -AATTTTTTTAATTTTTTTATGATTTTTATA
1 CAATTTTTATAATTTTTTTACGATTTTTATA
205642 TGTTTTAAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
45 3 0.05
46 17 0.26
47 39 0.59
48 2 0.03
49 5 0.08
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (46 bp):
CAATTTTTATAATTTTTTTACGATTTTTATAAAATTTTATAATTTT
Found at i:211238 original size:23 final size:24
Alignment explanation
Indices: 211203--211262 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
211193 TTATAGCAAA
211203 ATTTT-TTTCTTCTTATC-TTTTCTC
1 ATTTTCTTT-TTCTT-TCTTTTTCTC
211227 -TTTTCTTTTTCTTTCTTTTTCTC
1 ATTTTCTTTTTCTTTCTTTTTCTC
211250 ATTTTCCTTTTTC
1 ATTTT-CTTTTTC
211263 AAGTGACAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 2 0.06
23 16 0.50
24 7 0.22
25 7 0.22
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (24 bp):
ATTTTCTTTTTCTTTCTTTTTCTC
Found at i:211872 original size:16 final size:16
Alignment explanation
Indices: 211847--211883 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
211837 TTAACAAAAG
211847 AAATGAAATGACAATA
1 AAATGAAATGACAATA
*
211863 AAATGCAATGACAATA
1 AAATGAAATGACAATA
211879 AAATG
1 AAATG
211884 TATGCAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.08, G:0.14, T:0.19
Consensus pattern (16 bp):
AAATGAAATGACAATA
Found at i:214162 original size:15 final size:15
Alignment explanation
Indices: 214132--214160 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
214122 AAGTATTTAC
214132 AAGCATCATAAGTTT
1 AAGCATCATAAGTTT
214147 AAGCATC-TAAGTTT
1 AAGCATCATAAGTTT
214161 TACTTCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (15 bp):
AAGCATCATAAGTTT
Found at i:214577 original size:17 final size:17
Alignment explanation
Indices: 214555--214588 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
214545 AACATATGCG
214555 GTACCCTAACCATTGGT
1 GTACCCTAACCATTGGT
*
214572 GTACCCTAGCCATTGGT
1 GTACCCTAACCATTGGT
214589 ACAATGTCTA
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:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (17 bp):
GTACCCTAACCATTGGT
Found at i:216574 original size:21 final size:21
Alignment explanation
Indices: 216522--216574 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
216512 TATTCCTATG
* *
216522 TAAAATTTAAAACGAAATAAA
1 TAAAATGTAAAACAAAATAAA
216543 TAAAA-GTAAAACAAAATAAA
1 TAAAATGTAAAACAAAATAAA
216563 -AGAAATGTAAAA
1 TA-AAATGTAAAA
216575 ATGCGTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 16 0.57
21 11 0.39
ACGTcount: A:0.70, C:0.04, G:0.08, T:0.19
Consensus pattern (21 bp):
TAAAATGTAAAACAAAATAAA
Found at i:227185 original size:37 final size:37
Alignment explanation
Indices: 227130--227203 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
227120 TAATGTCACT
* ** * *
227130 GCATGAGTACTTTTAGATTGCGCCTAAAACTGTCGCC
1 GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCC
227167 GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCC
1 GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCC
227204 ATAGGAAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (37 bp):
GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCC
Found at i:227388 original size:26 final size:26
Alignment explanation
Indices: 227318--227388 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
227308 ATGTCTTTGT
* * *
227318 ATGAACATGTCCAGAATTATCGCTGC
1 ATGAACGTGTCCAGAATTGTCGCTAC
227344 ATGAACGTGTCCAGAATTGTCGCTAC
1 ATGAACGTGTCCAGAATTGTCGCTAC
*
227370 ATGAACGTGTCTAGAATTG
1 ATGAACGTGTCCAGAATTG
227389 CGCCCAGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (26 bp):
ATGAACGTGTCCAGAATTGTCGCTAC
Found at i:228426 original size:16 final size:16
Alignment explanation
Indices: 228402--228440 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
228392 GACATTCATA
*
228402 GCGCGATCAAGTTTTG
1 GCGCCATCAAGTTTTG
228418 GCGCCATCAAGTTTTG
1 GCGCCATCAAGTTTTG
*
228434 GTGCCAT
1 GCGCCAT
228441 TGCCGGGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (16 bp):
GCGCCATCAAGTTTTG
Found at i:230533 original size:17 final size:17
Alignment explanation
Indices: 230513--230549 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
230503 CTGTAGTATA
* *
230513 ATTGTCCCTGTATTTTT
1 ATTGTCACTGCATTTTT
230530 ATTGTCACTGCATTTTT
1 ATTGTCACTGCATTTTT
230547 ATT
1 ATT
230550 ATCGTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.57
Consensus pattern (17 bp):
ATTGTCACTGCATTTTT
Found at i:231659 original size:37 final size:37
Alignment explanation
Indices: 231604--231680 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
231594 TAATGTTGCT
* * ** *
231604 GCATGAGTACTTCTAGATTGTGCTCAAAACTATCGCC
1 GCATGAGCACTTCCAGATTGCACCCAAAACTATCGCC
*
231641 GCATGAGCACTTCCAGATTGCACCCAAAACTATCGTC
1 GCATGAGCACTTCCAGATTGCACCCAAAACTATCGCC
231678 GCA
1 GCA
231681 AGAATATTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (37 bp):
GCATGAGCACTTCCAGATTGCACCCAAAACTATCGCC
Found at i:231793 original size:37 final size:38
Alignment explanation
Indices: 231716--231793 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
231706 AATTTCACTA
* *
231716 CATAAATATTCTTCAAATTGCATCCAGAACTATCGCTG
1 CATAAATATTCTTCAAATTGCACCCAGAACTATCGATG
* *
231754 CATAAGTATTCTTC-AATTGCACCCAGGAA-TGTCGATG
1 CATAAATATTCTTCAAATTGCACCCA-GAACTATCGATG
231791 CAT
1 CAT
231794 GAACATGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 19 0.54
38 16 0.46
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (38 bp):
CATAAATATTCTTCAAATTGCACCCAGAACTATCGATG
Found at i:231835 original size:26 final size:26
Alignment explanation
Indices: 231783--231836 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
231773 CACCCAGGAA
*
231783 TGTCGATGCATGAACATGTCTAGAAT
1 TGTCGATGCATGAACATGTCCAGAAT
* *
231809 TGTCGTTGCATGAA-AGTGTCCATAAT
1 TGTCGATGCATGAACA-TGTCCAGAAT
231835 TG
1 TG
231837 CGCCCAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (26 bp):
TGTCGATGCATGAACATGTCCAGAAT
Found at i:233388 original size:25 final size:26
Alignment explanation
Indices: 233359--233410 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
233349 GTTTCACAAT
*
233359 TTCAGAAAT-ATATAGTTTG-GCTAAC
1 TTCAGAAATGA-ATAATTTGTGCTAAC
*
233384 TTCAGTAATGAATAATTTGTGCTAAC
1 TTCAGAAATGAATAATTTGTGCTAAC
233410 T
1 T
233411 GTAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (26 bp):
TTCAGAAATGAATAATTTGTGCTAAC
Found at i:240236 original size:26 final size:26
Alignment explanation
Indices: 240160--240237 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
240150 AGAAAGTTTA
* *
240160 GCTCATACGAGCCCAG-TCAATATAAT-
1 GCTCTTACGAG-CCAGTTCAGTAT-ATC
*
240186 GCTCTTACGAGCTAGTTCAGTATATC
1 GCTCTTACGAGCCAGTTCAGTATATC
240212 GCTCTTACGAGCCAGTTCAGTATATC
1 GCTCTTACGAGCCAGTTCAGTATATC
240238 AATCTTGTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.11
26 41 0.89
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (26 bp):
GCTCTTACGAGCCAGTTCAGTATATC
Found at i:240243 original size:26 final size:26
Alignment explanation
Indices: 240188--240243 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
240178 AATATAATGC
* **
240188 TCTTACGAGCTAGTTCAGTATATCGC
1 TCTTACGAGCCAGTTCAGTATATCAA
240214 TCTTACGAGCCAGTTCAGTATATCAA
1 TCTTACGAGCCAGTTCAGTATATCAA
240240 TCTT
1 TCTT
240244 GTTGCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (26 bp):
TCTTACGAGCCAGTTCAGTATATCAA
Found at i:240887 original size:12 final size:13
Alignment explanation
Indices: 240843--240905 Score: 60
Period size: 12 Copynumber: 5.1 Consensus size: 13
240833 CTAATCTCAA
240843 TTATTTTTATTGT
1 TTATTTTTATTGT
***
240856 TTA-TTTTAGCAT
1 TTATTTTTATTGT
*
240868 TTACTTTTATT-T
1 TTATTTTTATTGT
240880 TTATTTTT-TTGT
1 TTATTTTTATTGT
*
240892 TTATTTATATTGT
1 TTATTTTTATTGT
240905 T
1 T
240906 AATACTTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
11 2 0.05
12 25 0.62
13 13 0.32
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.73
Consensus pattern (13 bp):
TTATTTTTATTGT
Found at i:242771 original size:35 final size:35
Alignment explanation
Indices: 242725--242799 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
242715 GTGGCCGTGC
242725 GCATGTATCAGATTACTAGGATTTTACTCGGATTA
1 GCATGTATCAGATTACTAGGATTTTACTCGGATTA
242760 GCATGTATCAGATTACTAGGATTTTACTCGGATTA
1 GCATGTATCAGATTACTAGGATTTTACTCGGATTA
242795 GCATG
1 GCATG
242800 ACTCAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (35 bp):
GCATGTATCAGATTACTAGGATTTTACTCGGATTA
Found at i:247886 original size:46 final size:46
Alignment explanation
Indices: 247831--247918 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
247821 AAGTGGGTTT
* * * *
247831 GAGTTGAAAACTTGAAAGGGCGGCTCAAACTAGCAAAAAAAACTTC
1 GAGTTGAAAACCTAAAAGGGCAGCTCAAACCAGCAAAAAAAACTTC
* *
247877 GAGTTGAAAACCTAAAAGGGCAGTTTAAACCAGCAAAAAAAA
1 GAGTTGAAAACCTAAAAGGGCAGCTCAAACCAGCAAAAAAAA
247919 AAAAANAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (46 bp):
GAGTTGAAAACCTAAAAGGGCAGCTCAAACCAGCAAAAAAAACTTC
Found at i:247917 original size:1 final size:1
Alignment explanation
Indices: 247911--247971 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
247901 TTAAACCAGC
* * * * * * * *
247911 AAAAAAAAAAAAANAAAAGAAAAGAAAACAAAAGAAAAATAAAAAAAAATAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
247972 GGAGGTGTCG
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.02, G:0.07, T:0.03
Consensus pattern (1 bp):
A
Found at i:247933 original size:10 final size:9
Alignment explanation
Indices: 247911--247972 Score: 65
Period size: 10 Copynumber: 6.7 Consensus size: 9
247901 TTAAACCAGC
247911 AAAAA-AAA
1 AAAAAGAAA
*
247919 AAAAANAAA
1 AAAAAGAAA
247928 AGAAAAGAAA
1 A-AAAAGAAA
247938 ACAAAAGAAA
1 A-AAAAGAAA
247948 AATAAA-AAA
1 AA-AAAGAAA
247957 AAATAAGAAA
1 AAA-AAGAAA
247967 AAAAAG
1 AAAAAG
247973 GAGGTGTCGA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
8 6 0.13
9 15 0.32
10 26 0.55
ACGTcount: A:0.85, C:0.02, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:249081 original size:49 final size:49
Alignment explanation
Indices: 249012--249401 Score: 166
Period size: 49 Copynumber: 8.0 Consensus size: 49
249002 TCCTAGAGTT
* * * *
249012 GAAGAGGGATAGGTTCAAGCCGTAACGGCGGACTTAACACCCTAAAATC
1 GAAGAGGGAAAGATTGAAGCCGCAACGGCGGACTTAACACCCTAAAATC
* * * * *
249061 GAAGAGGGAAAGATTGAAGCCGCAACGGTGGATTTTACACCTTAAAATA
1 GAAGAGGGAAAGATTGAAGCCGCAACGGCGGACTTAACACCCTAAAATC
* * * * * * * * *
249110 AAAGAGGGATAGGTTGAAGTCACAATGGTGGACCTAATACCCTAAAA-C
1 GAAGAGGGAAAGATTGAAGCCGCAACGGCGGACTTAACACCCTAAAATC
* * *** *
249158 TGAAGAGGG-AAGAATTGAAGTCGCAATGATAGATCTT-ACACCTTAAAA-C
1 -GAAGAGGGAAAG-ATTGAAGCCGCAACGGCGGA-CTTAACACCCTAAAATC
** * * * * *
249207 TGAAGAGGGATAAG-TTGATA-CCATAACGGTGGACCTAACATCCAAAAATA
1 -GAAGAGGGA-AAGATTGA-AGCCGCAACGGCGGACTTAACACCCTAAAATC
* * * * * * ** * * * *
249257 AAAAAGGGATAGGTTGAAGCTGTAACAACGGACCTAAAACCTTAAAACC
1 GAAGAGGGAAAGATTGAAGCCGCAACGGCGGACTTAACACCCTAAAATC
* * * * * *
249306 AAAGAGGGAAAGATTGAAGTCGCAATGGCGAATCTT-ACACCTTAAAATT
1 GAAGAGGGAAAGATTGAAGCCGCAACGGCGGA-CTTAACACCCTAAAATC
* * * * *
249355 GAACAGGGATAGATTGAAGCCGTAACGACGAATCTT-ACACCCTAAAA
1 GAAGAGGGAAAGATTGAAGCCGCAACGGCGGA-CTTAACACCCTAAAA
249402 AATTGAACAG
Statistics
Matches: 253, Mismatches: 77, Indels: 22
0.72 0.22 0.06
Matches are distributed among these distances:
48 7 0.03
49 238 0.94
50 5 0.02
51 3 0.01
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (49 bp):
GAAGAGGGAAAGATTGAAGCCGCAACGGCGGACTTAACACCCTAAAATC
Found at i:249183 original size:98 final size:98
Alignment explanation
Indices: 249013--249401 Score: 266
Period size: 98 Copynumber: 4.0 Consensus size: 98
249003 CCTAGAGTTG
* ** *
249013 AAGAGGGATAGGTTCAAGCCGTAACGGCGGACTTAACACCCTAAAATCGAAGAGGGAAAGATTGA
1 AAGAGGGATAGGTTGAAGCCACAACGGCGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTGA
* * *
249078 AGCCGCAACGGTGGATTTTACACCTTAAAA-TAA
66 AGCCGCAACGATAGATCTTACACCTTAAAACT-A
* * * *
249111 AAGAGGGATAGGTTGAAGTCACAATGGTGGACCTAATACCCTAAAA-CTGAAGAGGG-AAGAATT
1 AAGAGGGATAGGTTGAAGCCACAACGGCGGACCTAACACCCTAAAATC-GAAGAGGGAAAG-ATT
* * *
249174 GAAGTCGCAATGATAGATCTTACACCTTAAAACTG
64 GAAGCCGCAACGATAGATCTTACACCTTAAAACTA
* * * * * ** * * *
249209 AAGAGGGATAAGTTGATA-CCATAACGGTGGACCTAACATCCAAAAATAAAAAAGGGATAGGTTG
1 AAGAGGGATAGGTTGA-AGCCACAACGGCGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTG
* * * ** * * * *
249273 AAGCTGTAACAACGGACCTAAAACCTTAAAACCA
65 AAGCCGCAACGATAGATCTTACACCTTAAAACTA
* * * * * * * * * * * *
249307 AAGAGGGAAAGATTGAAGTCGCAATGGCGAATCTTACACCTTAAAATTGAACAGGGATAGATTGA
1 AAGAGGGATAGGTTGAAGCCACAACGGCGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTGA
* * *
249372 AGCCGTAACGA-CGAATCTTACACCCTAAAA
66 AGCCGCAACGATAG-ATCTTACACCTTAAAA
249402 AATTGAACAG
Statistics
Matches: 220, Mismatches: 63, Indels: 16
0.74 0.21 0.05
Matches are distributed among these distances:
97 6 0.03
98 210 0.95
99 4 0.02
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (98 bp):
AAGAGGGATAGGTTGAAGCCACAACGGCGGACCTAACACCCTAAAATCGAAGAGGGAAAGATTGA
AGCCGCAACGATAGATCTTACACCTTAAAACTA
Found at i:249381 original size:147 final size:145
Alignment explanation
Indices: 249048--249381 Score: 356
Period size: 147 Copynumber: 2.3 Consensus size: 145
249038 GGCGGACTTA
* * * * ** * *
249048 ACACCCTAAAATCGAAGAGGGAAAGATTGAAGCCGCAACGGTGGATTTTACACCTTAAAATAAAA
1 ACACCTTAAAATTGAAGAGGGATAGATTGAAGCCGTAACGGTGGACCTAACACCTAAAAATAAAA
* * * * **
249113 GAGGGATAGGTTGAAGTCACAATGGTGGACCTAATACCCTAAAACTGAAGAGGGAAGAATTGAAG
66 AAGGGATAGGTTGAAGTAACAA--GCGGACCTAAAACCCTAAAACCAAAGAGGGAAGAATTGAAG
*
249178 TCGCAATGATAGATCTT
129 TCGCAATGAGAGATCTT
* *
249195 ACACCTTAAAACTGAAGAGGGATA-AGTTGATA-CCATAACGGTGGACCTAACATCC-AAAAATA
1 ACACCTTAAAATTGAAGAGGGATAGA-TTGA-AGCCGTAACGGTGGACCTAACA-CCTAAAAATA
*
249257 AAAAAGGGATAGGTTGAAGCTGTAACAA-CGGACCTAAAACCTTAAAACCAAAGAGGGAA-AGAT
63 AAAAAGGGATAGGTTGAA---GTAACAAGCGGACCTAAAACCCTAAAACCAAAGAGGGAAGA-AT
*
249320 TGAAGTCGCAATG-GCGAATCTT
124 TGAAGTCGCAATGAGAG-ATCTT
*
249342 ACACCTTAAAATTGAACAGGGATAGATTGAAGCCGTAACG
1 ACACCTTAAAATTGAAGAGGGATAGATTGAAGCCGTAACG
249382 ACGAATCTTA
Statistics
Matches: 155, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
146 4 0.03
147 141 0.91
148 4 0.03
150 6 0.04
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.19
Consensus pattern (145 bp):
ACACCTTAAAATTGAAGAGGGATAGATTGAAGCCGTAACGGTGGACCTAACACCTAAAAATAAAA
AAGGGATAGGTTGAAGTAACAAGCGGACCTAAAACCCTAAAACCAAAGAGGGAAGAATTGAAGTC
GCAATGAGAGATCTT
Found at i:249475 original size:45 final size:45
Alignment explanation
Indices: 249409--249716 Score: 332
Period size: 45 Copynumber: 6.8 Consensus size: 45
249399 AAAAATTGAA
*
249409 CAGATTGAAGTCACCACATCCAATCTTTTACCCCTAATCTAGAGGGG
1 CAGATTGAAGTCA-C-CATCCAATCTTTTACCCCTAATCCAGAGGGG
* * * *
249456 CAGATTGAAGCCACAATCCAGTCTTTTACCCCTAATCCAAAGGGG
1 CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATCCAGAGGGG
* * * * *
249501 TAGATTGAAATCATCATCCAATCTTTTACCCCTAATCTAGAGAGG
1 CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATCCAGAGGGG
* ** * * * *
249546 TAGATTGAAGTCACCATTTAATTTTTTACCTCTAATCAAGTGGGG
1 CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATCCAGAGGGG
* * * *
249591 CAGATTGAAG-CAATCATTCAATCTTTTACCCTTAATCCATAGGGG
1 CAGATTGAAGTC-ACCATCCAATCTTTTACCCCTAATCCAGAGGGG
* * * *
249636 CAGATTAAAGCCACCATCCAATTTTTTACCCCTAATCCAGA-AGG
1 CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATCCAGAGGGG
* *
249680 CAGATTGAAGTAACCATCCAGTCTTTTACCCCTAATC
1 CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATC
249717 TAAGAGGCAC
Statistics
Matches: 215, Mismatches: 44, Indels: 7
0.81 0.17 0.03
Matches are distributed among these distances:
44 35 0.16
45 166 0.77
46 2 0.01
47 12 0.06
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (45 bp):
CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATCCAGAGGGG
Found at i:249591 original size:135 final size:134
Alignment explanation
Indices: 249409--250009 Score: 528
Period size: 135 Copynumber: 4.6 Consensus size: 134
249399 AAAAATTGAA
* *
249409 CAGATTGAAGTCACCACATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCA-CAAT
1 CAGATTGAAGTCA-C-CATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCAATC-AT
* * * *
249473 CCAGTCTTTTACCCCTAATCCAAAGGGGTAGATTGAAA-TCATCATCCAATCTTTTACCCCTAAT
63 CCAATCTTTTACCCCTAATCCAAAGGGGCAGATT-AAAGCCACCATCCAATCTTTTACCCCTAAT
*
249537 CTAGAGAGG
127 CCAGA-AGG
* ** * * * *
249546 TAGATTGAAGTCACCATTTAATTTTTTACCTCTAATCAAGTGGGGCAGATTGAAGCAATCATTCA
1 CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCAATCATCCA
* * *
249611 ATCTTTTACCCTTAATCCATAGGGGCAGATTAAAGCCACCATCCAATTTTTTACCCCTAATCCAG
66 ATCTTTTACCCCTAATCCAAAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCCCTAATCCAG
249676 AAGG
131 AAGG
* * *
249680 CAGATTGAAGTAACCATCCAGTCTTTTACCCCTAATCTAAGA--GGC-------A-C--T-ATCT
1 CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATC-AAGAGGGGCAGATTGAAGCAATCATCC
* * * * * * * * *
249732 AGTCTTTTACTCCTAAT-CAAGAGGGGTAGATTGAAGCAACCATCTAGTCTTTTACCCGTAATGC
65 AATCTTTTACCCCTAATCCAA-AGGGGCAGATTAAAGCCACCATCCAATCTTTTACCCCTAATCC
249796 AG-A--
129 AGAAGG
* * * *
249799 -A-ATTGAA-TCCACCATCCAATCTTTTACCCCTAGTCAAGAAGGGTAGATTGAAGCAACCATCC
1 CAGATTGAAGT-CACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCAATCATCC
* * * * * * *
249861 AGTCTTTTA-CCCTAATCCAGAGGGGCAGATTGAAGCAACCATCCAGTCTTTTACCCTTAATCTA
65 AATCTTTTACCCCTAATCCAAAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCCCTAATCCA
*
249925 GAGGGG
130 GA-AGG
* * * * * *
249931 AAGATTGAAGCCACCATCCAATCATTTACCCCTAATCTAGAGGGGTAGATTAAAGCAATCATCCA
1 CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCAATCATCCA
*
249996 ATCTTTTATCCCTA
66 ATCTTTTACCCCTA
250010 TTCTATAGGT
Statistics
Matches: 376, Mismatches: 61, Indels: 56
0.76 0.12 0.11
Matches are distributed among these distances:
116 5 0.01
117 29 0.08
118 3 0.01
121 3 0.01
122 53 0.14
123 1 0.00
125 2 0.01
126 2 0.01
128 46 0.12
129 14 0.04
133 4 0.01
134 97 0.26
135 103 0.27
136 2 0.01
137 12 0.03
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (134 bp):
CAGATTGAAGTCACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCAATCATCCA
ATCTTTTACCCCTAATCCAAAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCCCTAATCCAG
AAGG
Found at i:249845 original size:84 final size:79
Alignment explanation
Indices: 249644--249967 Score: 267
Period size: 89 Copynumber: 3.9 Consensus size: 79
249634 GGCAGATTAA
* * * *
249644 AGCCACCATCCAATTTTTTACCCCTAATCCAGAA-GGCAGATTGAAGTAACCATCCAGTCTTTTA
1 AGCCACCATCCAATCTTTTACCCCTAATCAAGAAGGGTAGATTGAAGCAACCATCCAGTCTTTTA
*
249708 CCCCTAATC--TAAG
66 -CCCTAATCAGAAAG
* * * * * * *
249721 AGGCACTATCTAGTCTTTTACTCCTAATCAAGAGGGGTAGATTGAAGCAACCATCTAGTCTTTTA
1 AGCCACCATCCAATCTTTTACCCCTAATCAAGAAGGGTAGATTGAAGCAACCATCCAGTCTTTTA
249786 CCCGTAATGCAGAAATTG
66 CCC-TAAT-CAGAAA--G
* *
249804 AATCCACCATCCAATCTTTTACCCCTAGTCAAGAAGGGTAGATTGAAGCAACCATCCAGTCTTTT
1 -AGCCACCATCCAATCTTTTACCCCTAATCAAGAAGGGTAGATTGAAGCAACCATCCAGTCTTTT
249869 ACCCTAATCCAGAGGGGCAGATTG
65 ACCCTAAT-CAGA-----A-A--G
* * * * * * * * *
249893 AAGCAACCATCCAGTCTTTTACCCTTAATCTAGAGGGGAAGATTGAAGCCACCATCCAATCATTT
1 -AGCCACCATCCAATCTTTTACCCCTAATCAAGAAGGGTAGATTGAAGCAACCATCCAGTCTTTT
249958 ACCCCTAATC
65 A-CCCTAATC
249968 TAGAGGGGTA
Statistics
Matches: 199, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
77 29 0.15
78 31 0.16
79 1 0.01
81 2 0.01
83 9 0.05
84 59 0.30
88 1 0.01
89 60 0.30
90 7 0.04
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (79 bp):
AGCCACCATCCAATCTTTTACCCCTAATCAAGAAGGGTAGATTGAAGCAACCATCCAGTCTTTTA
CCCTAATCAGAAAG
Found at i:249867 original size:45 final size:45
Alignment explanation
Indices: 249732--250009 Score: 302
Period size: 45 Copynumber: 6.3 Consensus size: 45
249722 GGCACTATCT
* *
249732 AGTCTTTTACTCCTAATCAAGAGGGGTAGATTGAAGCAACCATCT
1 AGTCTTTTACCCCTAATCAAGAGGGGTAGATTGAAGCAACCATCC
* * *
249777 AGTCTTTTACCCGTAATGC-AGA-----A-ATTGAATCCACCATCC
1 AGTCTTTTACCCCTAAT-CAAGAGGGGTAGATTGAAGCAACCATCC
* * *
249816 AATCTTTTACCCCTAGTCAAGAAGGGTAGATTGAAGCAACCATCC
1 AGTCTTTTACCCCTAATCAAGAGGGGTAGATTGAAGCAACCATCC
* *
249861 AGTCTTTTA-CCCTAATCCAGAGGGGCAGATTGAAGCAACCATCC
1 AGTCTTTTACCCCTAATCAAGAGGGGTAGATTGAAGCAACCATCC
* * * *
249905 AGTCTTTTACCCTTAATCTAGAGGGGAAGATTGAAGCCACCATCC
1 AGTCTTTTACCCCTAATCAAGAGGGGTAGATTGAAGCAACCATCC
* * * * *
249950 AATCATTTACCCCTAATCTAGAGGGGTAGATTAAAGCAATCATCC
1 AGTCTTTTACCCCTAATCAAGAGGGGTAGATTGAAGCAACCATCC
* *
249995 AATCTTTTATCCCTA
1 AGTCTTTTACCCCTA
250010 TTCTATAGGT
Statistics
Matches: 196, Mismatches: 28, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.01
39 30 0.15
40 1 0.01
44 41 0.21
45 122 0.62
46 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (45 bp):
AGTCTTTTACCCCTAATCAAGAGGGGTAGATTGAAGCAACCATCC
Found at i:249940 original size:89 final size:88
Alignment explanation
Indices: 249734--250008 Score: 310
Period size: 89 Copynumber: 3.1 Consensus size: 88
249724 CACTATCTAG
* *
249734 TCTTTTACTCC-TAATCAAGAGGGGTAGATTGAAGCAACCATCTAGTCTTTTACCCGTAATGCAG
1 TCTTTTAC-CCTTAATCAAGAGGGGTAGATTGAAGCAACCATCCAGTCTTTTACCC-TAATCCAG
* *
249798 A----A-ATTGAATCCACCATCCAA
64 AGGGGAGATTGAAGCAACCATCCAA
* * *
249818 TCTTTTACCCCTAGTCAAGAAGGGTAGATTGAAGCAACCATCCAGTCTTTTACCCTAATCCAGAG
1 TCTTTTACCCTTAATCAAGAGGGGTAGATTGAAGCAACCATCCAGTCTTTTACCCTAATCCAGAG
*
249883 GGGCAGATTGAAGCAACCATCCAG
66 GGG-AGATTGAAGCAACCATCCAA
* * * * * *
249907 TCTTTTACCCTTAATCTAGAGGGGAAGATTGAAGCCACCATCCAATCATTTACCCCTAATCTAGA
1 TCTTTTACCCTTAATCAAGAGGGGTAGATTGAAGCAACCATCCAGTCTTTTA-CCCTAATCCAGA
* *
249972 GGGGTAGATTAAAGCAATCATCCAA
65 GGGG-AGATTGAAGCAACCATCCAA
249997 TCTTTTATCCCT
1 TCTTTTA-CCCT
250009 ATTCTATAGG
Statistics
Matches: 162, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
83 10 0.06
84 49 0.30
88 1 0.01
89 59 0.36
90 39 0.24
91 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (88 bp):
TCTTTTACCCTTAATCAAGAGGGGTAGATTGAAGCAACCATCCAGTCTTTTACCCTAATCCAGAG
GGGAGATTGAAGCAACCATCCAA
Found at i:249987 original size:134 final size:128
Alignment explanation
Indices: 249732--250009 Score: 360
Period size: 134 Copynumber: 2.1 Consensus size: 128
249722 GGCACTATCT
* *
249732 AGTCTTTTACTCCTAATCAAGAGGGGTAGATTGAAGCAACCATCTAGTCTTTTACCCGTAATGCA
1 AGTCTTTTAC-CCTAATCAAGAGGGGCAGATTGAAGCAACCATCCAGTCTTTTACCCGTAATGCA
* * * *
249797 GAAATTGAATCCACCATCCAATCTTTTACCCCTAGTCAAGAAGGGTAGATTGAAGCAACCATCC
65 GAAATTGAAGCCACCATCCAATCATTTACCCCTAATCAAGAAGGGTAGATTAAAGCAACCATCC
* *
249861 AGTCTTTTACCCTAATCCAGAGGGGCAGATTGAAGCAACCATCCAGTCTTTTACCCTTAAT-CTA
1 AGTCTTTTACCCTAATCAAGAGGGGCAGATTGAAGCAACCATCCAGTCTTTTACCCGTAATGC--
* * *
249925 GAGGGGAAGATTGAAGCCACCATCCAATCATTTACCCCTAATCTAGAGGGGTAGATTAAAGCAAT
64 -A---GAA-ATTGAAGCCACCATCCAATCATTTACCCCTAATCAAGAAGGGTAGATTAAAGCAAC
249990 CATCC
124 CATCC
*
249995 AATCTTTTATCCCTA
1 AGTCTTTTA-CCCTA
250010 TTCTATAGGT
Statistics
Matches: 129, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
127 1 0.01
128 47 0.36
129 10 0.08
130 1 0.01
133 3 0.02
134 62 0.48
135 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (128 bp):
AGTCTTTTACCCTAATCAAGAGGGGCAGATTGAAGCAACCATCCAGTCTTTTACCCGTAATGCAG
AAATTGAAGCCACCATCCAATCATTTACCCCTAATCAAGAAGGGTAGATTAAAGCAACCATCC
Found at i:256436 original size:21 final size:21
Alignment explanation
Indices: 256394--256433 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
256384 ATTTTTGTTA
*
256394 TTTACTTTTATTTGTTTCAAT
1 TTTACTTTTAGTTGTTTCAAT
256415 TTTACTTTT-GTTGTTTCAA
1 TTTACTTTTAGTTGTTTCAA
256434 ATTCCTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCAAT
Found at i:267266 original size:265 final size:265
Alignment explanation
Indices: 266791--267325 Score: 953
Period size: 265 Copynumber: 2.0 Consensus size: 265
266781 TCTCTATATC
266791 TGAGACTACCATTCCAAGGCTCTCTTTATCCATTTGCGAAATTTTCGAGAATTGCCCTTTACACG
1 TGAGACTACCATTCCAAGGCTCTCTTTATCCATTTGCGAAATTTTCGAGAATTGCCCTTTACACG
*
266856 ATAGGCCACCATGGATAATGTAATCCATTGAATAAAGATCTTTGAAAAATTGTACAACATGCTTT
66 ATAGGCCACCATGGATAATGTAATCCACTGAATAAAGATCTTTGAAAAATTGTACAACATGCTTT
* *
266921 TGTAACTCTGCCAACTCGAAACACCACTCCCCACCTTTGATTTTCAAGCCCTCAATTTTGTTATG
131 TGTAACTCTGCCAACTCAAAACACCACTCCCCACCTTCGATTTTCAAGCCCTCAATTTTGTTATG
*
266986 TTGTCGCCTAGCAAGTGTACGACCATGAAAAAACTTGATGTTCCTATCTCCATTAACAAGCCACT
196 TTGTCGCCAAGCAAGTGTACGACCATGAAAAAACTTGATGTTCCTATCTCCATTAACAAGCCACT
267051 TAGAA
261 TAGAA
* *
267056 TGAGACTACCATTCCAAGGCTCTCTTTATCCATTTGCGAAATTTTTGAGAATTGCCCTTTACATG
1 TGAGACTACCATTCCAAGGCTCTCTTTATCCATTTGCGAAATTTTCGAGAATTGCCCTTTACACG
267121 ATAGGCCACCATGGATAATGTAATCCACTGAATAAAGATCTTTGAAAAATTGTACAACATGCTTT
66 ATAGGCCACCATGGATAATGTAATCCACTGAATAAAGATCTTTGAAAAATTGTACAACATGCTTT
* * * * * * *
267186 TGTAACTTTGTCGATTCAAAACACCACTCCCCACCTTCGATTTTTAGGCCCTTAATTTTGTTATG
131 TGTAACTCTGCCAACTCAAAACACCACTCCCCACCTTCGATTTTCAAGCCCTCAATTTTGTTATG
267251 TTGTCGCCAAGCAAGTGTACGACCATGAAAAAACTTGATGTTCCTATCTCCATTAACAAGCCACT
196 TTGTCGCCAAGCAAGTGTACGACCATGAAAAAACTTGATGTTCCTATCTCCATTAACAAGCCACT
267316 TAGAA
261 TAGAA
267321 TGAGA
1 TGAGA
267326 TTTTTGGAAC
Statistics
Matches: 257, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
265 257 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (265 bp):
TGAGACTACCATTCCAAGGCTCTCTTTATCCATTTGCGAAATTTTCGAGAATTGCCCTTTACACG
ATAGGCCACCATGGATAATGTAATCCACTGAATAAAGATCTTTGAAAAATTGTACAACATGCTTT
TGTAACTCTGCCAACTCAAAACACCACTCCCCACCTTCGATTTTCAAGCCCTCAATTTTGTTATG
TTGTCGCCAAGCAAGTGTACGACCATGAAAAAACTTGATGTTCCTATCTCCATTAACAAGCCACT
TAGAA
Found at i:271962 original size:42 final size:42
Alignment explanation
Indices: 271907--272046 Score: 158
Period size: 42 Copynumber: 3.3 Consensus size: 42
271897 GAGGATTTGT
* * *
271907 ATTAATGGGAGACTCAAGTCTCGAAATGAGAATGAGAGTATG
1 ATTAAAGGAAGACTCAAGTCTCGAAATGAGAATGAGAATATG
*
271949 ATTAAAGGAAGACTCATA-TCTCGAGATGAGAATGAGAATATG
1 ATTAAAGGAAGACTCA-AGTCTCGAAATGAGAATGAGAATATG
* * * * * *
271991 AGTAAAGGAAGGCTCATGTCTTGGGAA-GATAATGAGAATATG
1 ATTAAAGGAAGACTCAAGTC-TCGAAATGAGAATGAGAATATG
272033 ATTAAAGGAAGACT
1 ATTAAAGGAAGACT
272047 TATGACTCGT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 78 0.95
43 4 0.05
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.24
Consensus pattern (42 bp):
ATTAAAGGAAGACTCAAGTCTCGAAATGAGAATGAGAATATG
Found at i:277061 original size:19 final size:19
Alignment explanation
Indices: 277039--277077 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
277029 GGAACCAGAC
277039 TAAATTTTAGCATTGCATA
1 TAAATTTTAGCATTGCATA
277058 TAAATTTTAGCATTGCATA
1 TAAATTTTAGCATTGCATA
277077 T
1 T
277078 CATCCATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (19 bp):
TAAATTTTAGCATTGCATA
Found at i:279165 original size:27 final size:27
Alignment explanation
Indices: 279135--279192 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
279125 ATATGATTAA
*
279135 AAGAAAACTTATGACTCGTTAGAGCAT
1 AAGAAAACTTATGACTAGTTAGAGCAT
*
279162 AAGAAGACTTATGACTAGTTAGAGCAT
1 AAGAAAACTTATGACTAGTTAGAGCAT
279189 AAGA
1 AAGA
279193 TTGATTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (27 bp):
AAGAAAACTTATGACTAGTTAGAGCAT
Found at i:285634 original size:12 final size:12
Alignment explanation
Indices: 285617--285719 Score: 97
Period size: 12 Copynumber: 8.9 Consensus size: 12
285607 ATAACATCCA
285617 AACAACAAAAAC
1 AACAACAAAAAC
*
285629 AACAACTAAAAC
1 AACAACAAAAAC
* * *
285641 AGCAGCAAAAAT
1 AACAACAAAAAC
285653 AACAAC--AAA-
1 AACAACAAAAAC
*
285662 AACAACAAAAAT
1 AACAACAAAAAC
*
285674 AACAGCAAAAAC
1 AACAACAAAAAC
*
285686 AACAACAAAAAT
1 AACAACAAAAAC
* *
285698 AACAGCAAAAGC
1 AACAACAAAAAC
285710 AAC-ACAAAAA
1 AACAACAAAAA
285720 TAGTAAAAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
9 6 0.08
10 3 0.04
11 8 0.11
12 55 0.76
ACGTcount: A:0.70, C:0.21, G:0.05, T:0.04
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:285640 original size:21 final size:21
Alignment explanation
Indices: 285603--285718 Score: 99
Period size: 24 Copynumber: 5.2 Consensus size: 21
285593 AAACGCATAA
* *
285603 AAAAATAACATC-CAAACAAC
1 AAAAATAACAACAAAAACAAC
* *
285623 AAAAACAACAACTAAAACAGCAGC
1 AAAAATAACAAC-AAAA-A-CAAC
285647 AAAAATAACAACAAAAACAAC
1 AAAAATAACAACAAAAACAAC
*
285668 AAAAATAACAGCAAAAACAACAAC
1 AAAAATAACA--ACAAA-AACAAC
* *
285692 AAAAATAACAGCAAAAGCAAC
1 AAAAATAACAACAAAAACAAC
285713 ACAAAA
1 A-AAAA
285719 ATAGTAAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
20 10 0.13
21 19 0.24
22 10 0.13
23 9 0.12
24 30 0.38
ACGTcount: A:0.69, C:0.22, G:0.04, T:0.05
Consensus pattern (21 bp):
AAAAATAACAACAAAAACAAC
Found at i:285651 original size:45 final size:45
Alignment explanation
Indices: 285603--285718 Score: 135
Period size: 45 Copynumber: 2.6 Consensus size: 45
285593 AAACGCATAA
* * * * *
285603 AAAAATAACATC-CAAACAACAAAAACAACAACTAAAACAGCAGC
1 AAAAATAACAACAAAAACAACAAAAACAACAACAAAAACAACAAC
* *
285647 AAAAATAACAACAAAAACAACAAAAATAACAGCAAAAACAACAAC
1 AAAAATAACAACAAAAACAACAAAAACAACAACAAAAACAACAAC
* *
285692 AAAAATAACAGCAAAAGCAACACAAAA
1 AAAAATAACAACAAAAACAACA-AAAA
285719 ATAGTAAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 11 0.18
45 46 0.75
46 4 0.07
ACGTcount: A:0.69, C:0.22, G:0.04, T:0.05
Consensus pattern (45 bp):
AAAAATAACAACAAAAACAACAAAAACAACAACAAAAACAACAAC
Found at i:285657 original size:33 final size:33
Alignment explanation
Indices: 285616--285719 Score: 113
Period size: 33 Copynumber: 3.1 Consensus size: 33
285606 AATAACATCC
* *
285616 AAACAACAA-AAACAACAACTAAAACAGCAGCAA
1 AAACAACAACAAA-AACAACAAAAACAACAGCAA
* *
285649 AAATAACAACAAAAACAACAAAAATAACAGCAA
1 AAACAACAACAAAAACAACAAAAACAACAGCAA
*
285682 AAACAACAACAAAAATAACAGCAAAAGCAACA-CAA
1 AAACAACAACAAAAACAACA--AAAA-CAACAGCAA
285717 AAA
1 AAA
285720 TAGTAAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
33 43 0.72
34 3 0.05
35 10 0.17
36 4 0.07
ACGTcount: A:0.70, C:0.21, G:0.05, T:0.04
Consensus pattern (33 bp):
AAACAACAACAAAAACAACAAAAACAACAGCAA
Found at i:285694 original size:24 final size:24
Alignment explanation
Indices: 285617--285721 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
285607 ATAACATCCA
* * *
285617 AACAACAAAAACAACAACTAAAAC
1 AACAACAAAAATAACAGCAAAAAC
* * *
285641 AGCAGCAAAAATAACA--ACAAA-
1 AACAACAAAAATAACAGCAAAAAC
285662 AACAACAAAAATAACAGCAAAAAC
1 AACAACAAAAATAACAGCAAAAAC
*
285686 AACAACAAAAATAACAGCAAAAGC
1 AACAACAAAAATAACAGCAAAAAC
285710 AAC-ACAAAAATA
1 AACAACAAAAATA
285722 GTAAAAAAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
21 14 0.20
22 3 0.04
23 13 0.19
24 39 0.57
ACGTcount: A:0.70, C:0.21, G:0.05, T:0.05
Consensus pattern (24 bp):
AACAACAAAAATAACAGCAAAAAC
Found at i:291224 original size:27 final size:26
Alignment explanation
Indices: 291176--291226 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
291166 AGATTTATTT
*
291176 AAAATAAAAATATTAAATTTAAATTA
1 AAAACAAAAATATTAAATTTAAATTA
291202 AAAACAAAAA-ATTATAATATTAAAT
1 AAAACAAAAATATTA-AAT-TTAAAT
291227 ATTTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAACAAAAATATTAAATTTAAATTA
Found at i:294948 original size:21 final size:21
Alignment explanation
Indices: 294931--294972 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
294921 TGGTTCTATT
294931 GATACAAGTATAACTTCTACC
1 GATACAAGTATAACTTCTACC
294952 GATACAAGTATAACTTCTACC
1 GATACAAGTATAACTTCTACC
294973 AAAACATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (21 bp):
GATACAAGTATAACTTCTACC
Found at i:295808 original size:42 final size:42
Alignment explanation
Indices: 295683--295941 Score: 221
Period size: 42 Copynumber: 6.1 Consensus size: 42
295673 GTCATATGCT
* * * * * ** *
295683 TTCCTTTAAACATAATCTCATGCTCTTTCAAAGTCACAAGTT
1 TTCCTTTAAACATAACCTCATGCTCATCCCAAGACATGAGTC
* * * * * * *
295725 TTCCTTTAAACATAATCTCATACTCTTTCTAAGTCACGAGTC
1 TTCCTTTAAACATAACCTCATGCTCATCCCAAGACATGAGTC
* * **
295767 TTCCTTTAAACATAATCTCATGCTCATCCCGACTCATGAGTC
1 TTCCTTTAAACATAACCTCATGCTCATCCCAAGACATGAGTC
* * * * * *
295809 TTCCTTTTAACATAACCTCACGCTTATCCTAAGACATGAATT
1 TTCCTTTAAACATAACCTCATGCTCATCCCAAGACATGAGTC
* * *
295851 TTCCTTTTTAAACATAACCTCATGCTTATCCCGAGACATGATTC
1 TTCC--TTTAAACATAACCTCATGCTCATCCCAAGACATGAGTC
*
295895 TTCCCTTTTAAACATAACCTCATGCTCATCCCGAGACATGAGTC
1 TT-CC-TTTAAACATAACCTCATGCTCATCCCAAGACATGAGTC
295939 TTC
1 TTC
295942 TATTTATACG
Statistics
Matches: 185, Mismatches: 29, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
42 109 0.59
43 1 0.01
44 73 0.39
45 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (42 bp):
TTCCTTTAAACATAACCTCATGCTCATCCCAAGACATGAGTC
Found at i:295884 original size:86 final size:88
Alignment explanation
Indices: 295771--295935 Score: 235
Period size: 86 Copynumber: 1.9 Consensus size: 88
295761 CGAGTCTTCC
* * *
295771 TTTAAACATAATCTCATGCTCATCCCGACTCATGAGTCTT-CCTTTT-AACATAACCTCACGCTT
1 TTTAAACATAACCTCATGCTCATCCCGACACATGAGTCTTCCCTTTTAAACATAACCTCACGCTC
*
295834 ATCCTAAGACATGAATTTTCCTT
66 ATCCCAAGACATGAATTTTCCTT
* * * *
295857 TTTAAACATAACCTCATGCTTATCCCGAGACATGATTCTTCCCTTTTAAACATAACCTCATGCTC
1 TTTAAACATAACCTCATGCTCATCCCGACACATGAGTCTTCCCTTTTAAACATAACCTCACGCTC
*
295922 ATCCCGAGACATGA
66 ATCCCAAGACATGA
295936 GTCTTCTATT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
86 35 0.51
87 6 0.09
88 27 0.40
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.33
Consensus pattern (88 bp):
TTTAAACATAACCTCATGCTCATCCCGACACATGAGTCTTCCCTTTTAAACATAACCTCACGCTC
ATCCCAAGACATGAATTTTCCTT
Found at i:295941 original size:44 final size:44
Alignment explanation
Indices: 295762--295941 Score: 224
Period size: 44 Copynumber: 4.2 Consensus size: 44
295752 TCTAAGTCAC
* **
295762 GAGTCTT-CC-TTTAAACATAATCTCATGCTCATCCCGACTCAT
1 GAGTCTTCCCTTTTAAACATAACCTCATGCTCATCCCGAGACAT
* * **
295804 GAGTCTT-CCTTTT-AACATAACCTCACGCTTATCCTAAGACAT
1 GAGTCTTCCCTTTTAAACATAACCTCATGCTCATCCCGAGACAT
* * * *
295846 GAATTTTCCTTTTTAAACATAACCTCATGCTTATCCCGAGACAT
1 GAGTCTTCCCTTTTAAACATAACCTCATGCTCATCCCGAGACAT
*
295890 GATTCTTCCCTTTTAAACATAACCTCATGCTCATCCCGAGACAT
1 GAGTCTTCCCTTTTAAACATAACCTCATGCTCATCCCGAGACAT
295934 GAGTCTTC
1 GAGTCTTC
295942 TATTTATACG
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
42 36 0.31
43 8 0.07
44 73 0.62
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (44 bp):
GAGTCTTCCCTTTTAAACATAACCTCATGCTCATCCCGAGACAT
Found at i:300547 original size:21 final size:21
Alignment explanation
Indices: 300521--300596 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 21
300511 TTGAGTTAAA
300521 TATTTTCAAACATGTTAAAAC
1 TATTTTCAAACATGTTAAAAC
* *
300542 TATTTT-AAAGCAAGTCAGTATAGTTAAA
1 TATTTTCAAA-C-A-T--GT-TA--AAAC
300570 TATTTTCAAACATGTTAAAAC
1 TATTTTCAAACATGTTAAAAC
300591 TATTTT
1 TATTTT
300597 AAAGCAAGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
20 3 0.07
21 15 0.36
22 1 0.02
23 3 0.07
24 2 0.05
25 2 0.05
26 3 0.07
27 1 0.02
28 9 0.21
29 3 0.07
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (21 bp):
TATTTTCAAACATGTTAAAAC
Found at i:300568 original size:30 final size:30
Alignment explanation
Indices: 300534--300615 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 30
300524 TTTCAAACAT
300534 GTTAAAACTATTTTAAAGCAAGTCAGTATA
1 GTTAAAACTATTTTAAAGCAAGTCAGTATA
*
300564 GTT-AAA-TATTTT----CAA---A-CAT-
1 GTTAAAACTATTTTAAAGCAAGTCAGTATA
300583 GTTAAAACTATTTTAAAGCAAGTCAGTATA
1 GTTAAAACTATTTTAAAGCAAGTCAGTATA
300613 GTT
1 GTT
300616 TCAAGCCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 22
0.62 0.03 0.35
Matches are distributed among these distances:
19 3 0.08
20 5 0.13
21 7 0.18
24 3 0.08
25 3 0.08
28 7 0.18
29 5 0.13
30 6 0.15
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (30 bp):
GTTAAAACTATTTTAAAGCAAGTCAGTATA
Found at i:300572 original size:49 final size:49
Alignment explanation
Indices: 300514--300615 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
300504 GTTTCAATTG
300514 AGTTAAATATTTTCAAACATGTTAAAACTATTTTAAAGCAAGTCAGTAT
1 AGTTAAATATTTTCAAACATGTTAAAACTATTTTAAAGCAAGTCAGTAT
300563 AGTTAAATATTTTCAAACATGTTAAAACTATTTTAAAGCAAGTCAGTAT
1 AGTTAAATATTTTCAAACATGTTAAAACTATTTTAAAGCAAGTCAGTAT
300612 AGTT
1 AGTT
300616 TCAAGCCAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (49 bp):
AGTTAAATATTTTCAAACATGTTAAAACTATTTTAAAGCAAGTCAGTAT
Found at i:301277 original size:38 final size:39
Alignment explanation
Indices: 301229--301307 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 39
301219 AGTCTTAAAG
* * *
301229 TTTGGGTAGAAACCTTAAGGGAG-TTGCAATATTAAGAT
1 TTTGGATAGAAACCTTAAGGGAGATTGCAAAATTAAAAT
* *
301267 TTTGGATAGAAATCTTAAGGGAGATTGTAAAATTAAAAT
1 TTTGGATAGAAACCTTAAGGGAGATTGCAAAATTAAAAT
301306 TT
1 TT
301308 GTCCTCAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
38 21 0.60
39 14 0.40
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (39 bp):
TTTGGATAGAAACCTTAAGGGAGATTGCAAAATTAAAAT
Found at i:305327 original size:23 final size:25
Alignment explanation
Indices: 305301--305357 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
305291 TTTCTTACTC
305301 TTTTCTTTTTGTAT-TTTT-ACTT-A
1 TTTTCTTTTTGT-TCTTTTCACTTGA
* *
305324 TTTTCATTTTGTTCTTTTCACTTGT
1 TTTTCTTTTTGTTCTTTTCACTTGA
305349 TTTTCTTTT
1 TTTTCTTTT
305358 CTTTGGCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.04
23 15 0.54
24 4 0.14
25 8 0.29
ACGTcount: A:0.09, C:0.12, G:0.05, T:0.74
Consensus pattern (25 bp):
TTTTCTTTTTGTTCTTTTCACTTGA
Found at i:305341 original size:24 final size:23
Alignment explanation
Indices: 305301--305351 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
305291 TTTCTTACTC
* *
305301 TTTTCTTTTTGTATTTTTACTTA
1 TTTTCATTTTGTATTTTCACTTA
* *
305324 TTTTCATTTTGTTCTTTTCACTTG
1 TTTTCATTTTG-TATTTTCACTTA
305348 TTTT
1 TTTT
305352 TCTTTTCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.10, C:0.12, G:0.06, T:0.73
Consensus pattern (23 bp):
TTTTCATTTTGTATTTTCACTTA
Found at i:312514 original size:33 final size:33
Alignment explanation
Indices: 312477--312543 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
312467 CAGAACTGAA
*
312477 ACCATCACCGGTTACGATCCCAGGGTGTTTCAG
1 ACCATCACCAGTTACGATCCCAGGGTGTTTCAG
* * *
312510 ACCATCGCTAGTTACGGTCCCAGGGTGTTTCAG
1 ACCATCACCAGTTACGATCCCAGGGTGTTTCAG
312543 A
1 A
312544 TCATTTACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.25
Consensus pattern (33 bp):
ACCATCACCAGTTACGATCCCAGGGTGTTTCAG
Found at i:312785 original size:21 final size:21
Alignment explanation
Indices: 312761--312804 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
312751 CTACTGGTAG
312761 AAGTGAAGGTT-CTACCGATAC
1 AAGT-AAGGTTACTACCGATAC
*
312782 AAGTATGGTTACTACCGATAC
1 AAGTAAGGTTACTACCGATAC
312803 AA
1 AA
312805 TCCACACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (21 bp):
AAGTAAGGTTACTACCGATAC
Found at i:313548 original size:25 final size:25
Alignment explanation
Indices: 313513--313671 Score: 219
Period size: 25 Copynumber: 6.4 Consensus size: 25
313503 AACCCAAACG
*
313513 GAATATCGCTCTTACGATCCAGACA
1 GAATATCGCTCTTACGAGCCAGACA
* * *
313538 GAATATTGCTCTTACGAGCTAGACT
1 GAATATCGCTCTTACGAGCCAGACA
* *
313563 GAATATCGCTCTTATGAGCTAGACA
1 GAATATCGCTCTTACGAGCCAGACA
* *
313588 GAATATCGCTCTTACGACCCAGATA
1 GAATATCGCTCTTACGAGCCAGACA
* *
313613 GAATATCACTCTTACGAGCCAGAAA
1 GAATATCGCTCTTACGAGCCAGACA
*
313638 GAATATCGCTCTTACGAGCCAGATA
1 GAATATCGCTCTTACGAGCCAGACA
313663 GAATATCGC
1 GAATATCGC
313672 CCCACTGAGC
Statistics
Matches: 118, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 118 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (25 bp):
GAATATCGCTCTTACGAGCCAGACA
Found at i:324429 original size:37 final size:37
Alignment explanation
Indices: 324381--324676 Score: 387
Period size: 37 Copynumber: 8.0 Consensus size: 37
324371 CTTACACAAT
* *
324381 TTTTCAGGCTTTGTGCCTAGTAAGCTTCGTGTCGGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* * * *
324418 TTTTCAAGCTTTGTGCCTATTAGGCTTTGTGCTGGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* * *
324455 TCTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCTGGTA
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* *
324492 TTTTCAGGCTTTGTGCCTAGTAGGTTTCCTGCCGGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* * *
324529 TTTTCAAGCTTTGTGCCTAGTAGGCATCCTGCCGGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* *
324566 TTTTCAGGCTTTGTGCCTAGTAGGCTTCATGCCAGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* *
324603 TTTTCAGGCTTTGTGCCTAGTAGGCTTCATGCCGATG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* * *
324640 TATT-AGGGTTATGTGCCTAGTAGGCTTTGTGCCGGTG
1 TTTTCAGGCTT-TGTGCCTAGTAGGCTTCGTGCCGGTG
324677 ATCCAAGAAC
Statistics
Matches: 228, Mismatches: 30, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
36 5 0.02
37 223 0.98
ACGTcount: A:0.12, C:0.20, G:0.29, T:0.39
Consensus pattern (37 bp):
TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
Found at i:330517 original size:37 final size:37
Alignment explanation
Indices: 330467--330572 Score: 142
Period size: 37 Copynumber: 2.9 Consensus size: 37
330457 GGAGTAGAAG
*
330467 AGGCTTTGTGCCTAGTAGACTTTGTGTCGGTGT-TTT
1 AGGCTATGTGCCTAGTAGACTTTGTGTCGGTGTATTT
* *
330503 CAGGCTATGTGCCTAGTAGACTTCGTGTCGATGTATTT
1 -AGGCTATGTGCCTAGTAGACTTTGTGTCGGTGTATTT
* * *
330541 GGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
1 AGGCTATGTGCCTAGTAGACTTTGTGTCGGTG
330573 ATCCAAGAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
37 57 0.95
38 3 0.05
ACGTcount: A:0.13, C:0.17, G:0.32, T:0.38
Consensus pattern (37 bp):
AGGCTATGTGCCTAGTAGACTTTGTGTCGGTGTATTT
Found at i:334042 original size:18 final size:18
Alignment explanation
Indices: 334019--334103 Score: 98
Period size: 18 Copynumber: 4.4 Consensus size: 18
334009 GAACAATGAC
334019 TTGCATTGTTATTTGTCA
1 TTGCATTGTTATTTGTCA
*
334037 TTGCATTTTTATTTGTCA
1 TTGCATTGTTATTTGTCA
*
334055 TTGTCATTGTCATTGTCATTGTCA
1 TTG-CATTG---TTAT--TTGTCA
334079 TTGCATTGTTATTTGTCA
1 TTGCATTGTTATTTGTCA
334097 TTGCATT
1 TTGCATT
334104 TTTCATTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
18 33 0.58
19 4 0.07
20 3 0.05
22 3 0.05
23 5 0.09
24 9 0.16
ACGTcount: A:0.16, C:0.13, G:0.15, T:0.55
Consensus pattern (18 bp):
TTGCATTGTTATTTGTCA
Found at i:334058 original size:6 final size:6
Alignment explanation
Indices: 334031--334103 Score: 80
Period size: 6 Copynumber: 12.3 Consensus size: 6
334021 GCATTGTTAT
* *
334031 TTGTCA TTG-CA TTTTTA TTTGTCA TTGTCA TTGTCA TTGTCA TTGTCA
1 TTGTCA TTGTCA TTGTCA -TTGTCA TTGTCA TTGTCA TTGTCA TTGTCA
*
334079 TTG-CA TTGTTA TTTGTCA TTG-CA TT
1 TTGTCA TTGTCA -TTGTCA TTGTCA TT
334104 TTTCATTATA
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
5 13 0.23
6 35 0.61
7 9 0.16
ACGTcount: A:0.16, C:0.14, G:0.15, T:0.55
Consensus pattern (6 bp):
TTGTCA
Found at i:340643 original size:29 final size:29
Alignment explanation
Indices: 340590--340687 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 29
340580 CTACTATTTT
* * **
340590 TTTTCTAGATTTTATAGTTAAGCCACTAG
1 TTTTCTAGATTTTACAATTCTGCCACTAG
** *
340619 TTTTCTCTATTTTACAGTTCTGCCACT-G
1 TTTTCTAGATTTTACAATTCTGCCACTAG
*
340647 CTTTT-TAGATTTTACAATTTTGCCACTAG
1 -TTTTCTAGATTTTACAATTCTGCCACTAG
340676 TTTTC-AGATTTT
1 TTTTCTAGATTTT
340688 TTAGTTCTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 30 0.53
29 27 0.47
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.50
Consensus pattern (29 bp):
TTTTCTAGATTTTACAATTCTGCCACTAG
Done.