Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 123 of 202
Found at i:38132454 original size:41 final size:41
Alignment explanation
Indices: 38132416--38132521 Score: 140
Period size: 41 Copynumber: 2.6 Consensus size: 41
38132406 CCGACATAAG
* *
38132416 TAACATAATACATAGCTTACATAATACACAACTTACATAGC
1 TAACATAATACATAACTTACATAAAACACAACTTACATAGC
* * * *
38132457 TTACATACTAAATAACTTACATAAAATACAACTTACATAGC
1 TAACATAATACATAACTTACATAAAACACAACTTACATAGC
* *
38132498 TCACATAATACGTAACTTACATAA
1 TAACATAATACATAACTTACATAA
38132522 CTTATATAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (41 bp):
TAACATAATACATAACTTACATAAAACACAACTTACATAGC
Found at i:38132473 original size:25 final size:25
Alignment explanation
Indices: 38132424--38132479 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
38132414 AGTAACATAA
*
38132424 TACATAGCTTACATAATACACAACT
1 TACATAGCTTACATAATAAACAACT
* *
38132449 TACATAGCTTACATACTAAATAACT
1 TACATAGCTTACATAATAAACAACT
38132474 TACATA
1 TACATA
38132480 AAATACAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (25 bp):
TACATAGCTTACATAATAAACAACT
Found at i:38132534 original size:16 final size:16
Alignment explanation
Indices: 38132449--38132547 Score: 67
Period size: 16 Copynumber: 6.1 Consensus size: 16
38132439 ATACACAACT
* *
38132449 TACATAGCTTACATAC
1 TACATAACTTACATAA
*
38132465 TAAATAACTTACATAA
1 TACATAACTTACATAA
* * * *
38132481 AATACAACTTACATAGC
1 TACATAACTTACATA-A
*
38132498 TCACATAA--TACGTAA
1 T-ACATAACTTACATAA
*
38132513 CTTACATAACTTATATAA
1 --TACATAACTTACATAA
38132531 TACATAACTTACATAA
1 TACATAACTTACATAA
38132547 T
1 T
38132548 TTACTTAATA
Statistics
Matches: 62, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
16 52 0.84
17 1 0.02
18 9 0.15
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:38132556 original size:25 final size:25
Alignment explanation
Indices: 38132468--38132559 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 25
38132458 TACATACTAA
* * * *
38132468 ATAACTTACATAAAATACAACTTAC
1 ATAACTTATATAATACATAACTTAC
* * * *
38132493 ATAGCTCACATAATACGTAACTTAC
1 ATAACTTATATAATACATAACTTAC
38132518 ATAACTTATATAATACATAACTTAC
1 ATAACTTATATAATACATAACTTAC
*
38132543 ATAATTTACT-TAATACA
1 ATAACTTA-TATAATACA
38132560 GAAATATATA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 54 0.98
26 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (25 bp):
ATAACTTATATAATACATAACTTAC
Found at i:38135475 original size:43 final size:43
Alignment explanation
Indices: 38135413--38135639 Score: 298
Period size: 43 Copynumber: 5.3 Consensus size: 43
38135403 TCTGCCAAAA
* *
38135413 TTAGCGGCGTTTGTGGGAGAAGCGCCGCTAACGGTCTTGGTCT
1 TTAGCGGCGTTTGTAGGAGAAGCGCCGCTAAAGGTCTTGGTCT
* * *
38135456 TTAGCGGCGTTTGTAGGAGAAGTGCTGCTAAAGGTCTTGGTTT
1 TTAGCGGCGTTTGTAGGAGAAGCGCCGCTAAAGGTCTTGGTCT
** *
38135499 TTAGCGGCGTTTGTAAAAGAAGCGTCGCTAAAGGTCTTGGTCT
1 TTAGCGGCGTTTGTAGGAGAAGCGCCGCTAAAGGTCTTGGTCT
*
38135542 TTAGCGGCGTTTGT-GGA-ATTAGTGCCGCTAAAGGTCTTGGTCT
1 TTAGCGGCGTTTGTAGGAGA--AGCGCCGCTAAAGGTCTTGGTCT
* *
38135585 TTAGCGGCGTTTGTGTGGA-AAGCGCCGCTAAAGGTCTTGATCT
1 TTAGCGGCGTTTGT-AGGAGAAGCGCCGCTAAAGGTCTTGGTCT
*
38135628 TTAGCGACGTTT
1 TTAGCGGCGTTT
38135640 TTTTGTGGAA
Statistics
Matches: 162, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 156 0.96
45 4 0.02
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTGTAGGAGAAGCGCCGCTAAAGGTCTTGGTCT
Found at i:38135882 original size:40 final size:40
Alignment explanation
Indices: 38135838--38135918 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
38135828 GCCTGAATGC
38135838 AAGCATTTTCATTATATTTTAGTTAGGTTTATTTAGTTTT
1 AAGCATTTTCATTATATTTTAGTTAGGTTTATTTAGTTTT
38135878 AAGCATTTTCATTATATTTTAGTTAGGTTTATTTAGTTTT
1 AAGCATTTTCATTATATTTTAGTTAGGTTTATTTAGTTTT
38135918 A
1 A
38135919 CTTACATTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (40 bp):
AAGCATTTTCATTATATTTTAGTTAGGTTTATTTAGTTTT
Found at i:38135897 original size:20 final size:20
Alignment explanation
Indices: 38135838--38135898 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
38135828 GCCTGAATGC
38135838 AAGCATTTTCATTATATTTT
1 AAGCATTTTCATTATATTTT
* *
38135858 -AGTTAGGTTT-ATT-TAGTTTT
1 AAG-CA-TTTTCATTATA-TTTT
38135878 AAGCATTTTCATTATATTTT
1 AAGCATTTTCATTATATTTT
38135898 A
1 A
38135899 GTTAGGTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
19 7 0.23
20 17 0.55
21 7 0.23
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.56
Consensus pattern (20 bp):
AAGCATTTTCATTATATTTT
Found at i:38135917 original size:20 final size:20
Alignment explanation
Indices: 38135854--38135918 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
38135844 TTTCATTATA
38135854 TTTTAGTTAGGTTTATTTAG
1 TTTTAGTTAGGTTTATTTAG
* *
38135874 TTTTAAG-CA-TTTTCATTATA-
1 TTTT-AGTTAGGTTT-ATT-TAG
38135894 TTTTAGTTAGGTTTATTTAG
1 TTTTAGTTAGGTTTATTTAG
38135914 TTTTA
1 TTTTA
38135919 CTTACATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
19 7 0.20
20 21 0.60
21 7 0.20
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.60
Consensus pattern (20 bp):
TTTTAGTTAGGTTTATTTAG
Found at i:38141059 original size:14 final size:14
Alignment explanation
Indices: 38141042--38141072 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
38141032 ACATAAGCAG
38141042 TCACTAAGGTTCAC
1 TCACTAAGGTTCAC
38141056 TCACTAAGGTTCAC
1 TCACTAAGGTTCAC
38141070 TCA
1 TCA
38141073 AAGCATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (14 bp):
TCACTAAGGTTCAC
Found at i:38142300 original size:5 final size:5
Alignment explanation
Indices: 38142290--38142372 Score: 53
Period size: 5 Copynumber: 15.4 Consensus size: 5
38142280 TAAAGTGCAT
* **
38142290 AATAA AATAA AATAA AATAA TATAA GTCTGAAA AATAA AA-AA AATAA
1 AATAA AATAA AATAA AATAA AATAA -AAT--AA AATAA AATAA AATAA
38142337 CAATAAA AATAA AAGTACA AATAA AA-AA ACATAA AA
1 -AAT-AA AATAA AA-TA-A AATAA AATAA A-ATAA AA
38142373 CATAAAACTA
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
4 7 0.11
5 34 0.53
6 15 0.23
7 6 0.09
8 2 0.03
ACGTcount: A:0.73, C:0.05, G:0.04, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:38150595 original size:21 final size:21
Alignment explanation
Indices: 38150571--38150616 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
38150561 CTCCGAATGC
*
38150571 CCCTTCCTCCTTTC-TCTTCTT
1 CCCTTCC-CCTTCCTTCTTCTT
*
38150592 CCCTTTCCCTTCCTTCTTCTT
1 CCCTTCCCCTTCCTTCTTCTT
38150613 CCCT
1 CCCT
38150617 CATCAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (21 bp):
CCCTTCCCCTTCCTTCTTCTT
Found at i:38151042 original size:20 final size:22
Alignment explanation
Indices: 38150998--38151051 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
38150988 GTTTTTGGAT
*
38150998 TTATTATTTATTTTTCTTATTTC
1 TTATT-TTTATTTTTCTTATATC
38151021 TTATTTTTATTTTTC-TA-ATC
1 TTATTTTTATTTTTCTTATATC
*
38151041 TTTTTTTTATT
1 TTATTTTTATT
38151052 ATTCCTATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.41
21 2 0.07
22 10 0.34
23 5 0.17
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTTTTATTTTTCTTATATC
Found at i:38151196 original size:26 final size:26
Alignment explanation
Indices: 38151167--38151231 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
38151157 TTTATTTTTA
38151167 TTTTTAGTATTATTCA-TTGTTGGTTC
1 TTTTTAGTATTATTCAGTT-TTGGTTC
* * *
38151193 TTTTTATTATTACTCAGTTTTGTTTC
1 TTTTTAGTATTATTCAGTTTTGGTTC
*
38151219 -TTTTGGTATTATT
1 TTTTTAGTATTATT
38151232 TTTCTAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 10 0.31
26 20 0.62
27 2 0.06
ACGTcount: A:0.15, C:0.08, G:0.12, T:0.65
Consensus pattern (26 bp):
TTTTTAGTATTATTCAGTTTTGGTTC
Found at i:38159028 original size:20 final size:20
Alignment explanation
Indices: 38159000--38159038 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38158990 GCTACTCATA
*
38159000 TTTTTAAAA-ACTTATCAGAG
1 TTTTCAAAACACTTA-CAGAG
38159020 TTTTCAAAACACTTACAGA
1 TTTTCAAAACACTTACAGA
38159039 ATCGGTGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (20 bp):
TTTTCAAAACACTTACAGAG
Found at i:38162515 original size:19 final size:19
Alignment explanation
Indices: 38162493--38162534 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
38162483 TTCTTTTCAG
38162493 TTTCAGTTTCATTTTTAA-T
1 TTTCAGTTTC-TTTTTAAGT
**
38162512 TTTCTTTTTCTTTTTAAGT
1 TTTCAGTTTCTTTTTAAGT
38162531 TTTC
1 TTTC
38162535 TTTTTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTCAGTTTCTTTTTAAGT
Found at i:38162535 original size:19 final size:19
Alignment explanation
Indices: 38162499--38162539 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
38162489 TCAGTTTCAG
38162499 TTTCATTTTTAATTTTCTT
1 TTTCATTTTTAATTTTCTT
38162518 TTTC-TTTTTAAGTTTTCTT
1 TTTCATTTTTAA-TTTTCTT
38162537 TTT
1 TTT
38162540 TTAGTTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTCATTTTTAATTTTCTT
Found at i:38170762 original size:27 final size:27
Alignment explanation
Indices: 38170732--38170797 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
38170722 CCTCACGTGG
38170732 TAAAATGACTGTTATGCCCCTATGCTA
1 TAAAATGACTGTTATGCCCCTATGCTA
* * * *
38170759 TAAAATGACTATTATTCCCTTATGTTA
1 TAAAATGACTGTTATGCCCCTATGCTA
38170786 TAAAATGACTGT
1 TAAAATGACTGT
38170798 ATGATTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (27 bp):
TAAAATGACTGTTATGCCCCTATGCTA
Found at i:38178062 original size:26 final size:27
Alignment explanation
Indices: 38177925--38178047 Score: 178
Period size: 27 Copynumber: 4.6 Consensus size: 27
38177915 CCCTAAACTA
* *
38177925 TTATAAAATGACTATTATG-CCCTCACG
1 TTATAAAATGACTGTTATGCCCCT-ATG
38177952 -TAGTAAAATGACTGTTATGCCCCTATG
1 TTA-TAAAATGACTGTTATGCCCCTATG
*
38177979 TTATAAAATAACTGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
*
38178006 TTATAAAATGACAGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
38178033 TTATAAAATGACTGT
1 TTATAAAATGACTGT
38178048 ATGATTTTAT
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.02
27 79 0.91
28 6 0.07
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (27 bp):
TTATAAAATGACTGTTATGCCCCTATG
Found at i:38180365 original size:24 final size:26
Alignment explanation
Indices: 38180332--38180384 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
38180322 TTTAATTATA
38180332 ATTTAATATAAACACAT-ATAATATT
1 ATTTAATATAAACACATAATAATATT
*
38180357 ATTT-ATATAAACATATAAATAATATT
1 ATTTAATATAAACACAT-AATAATATT
38180383 AT
1 AT
38180385 ACTTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 11 0.44
25 4 0.16
26 10 0.40
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
ATTTAATATAAACACATAATAATATT
Found at i:38181667 original size:20 final size:20
Alignment explanation
Indices: 38181642--38181681 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38181632 AATATTTTTC
*
38181642 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
38181662 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
38181682 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:38181683 original size:34 final size:35
Alignment explanation
Indices: 38181630--38181696 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
38181620 CAAACACCAG
* *
38181630 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
38181665 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
38181697 TATTTTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:38197827 original size:48 final size:49
Alignment explanation
Indices: 38197741--38197833 Score: 152
Period size: 48 Copynumber: 1.9 Consensus size: 49
38197731 TTTTGGAGGC
* *
38197741 ACCAACTTTCAATGAATTATTTTTTAGTGTTAATTCTAGATGTGAAGGT
1 ACCAACTTTCAATGAATTATCTTTTAGTGTTAACTCTAGATGTGAAGGT
*
38197790 ACCAACTTTCAATGGATTA-CTTTTAGTGTTAACTCTAGATGTGA
1 ACCAACTTTCAATGAATTATCTTTTAGTGTTAACTCTAGATGTGA
38197834 CGACACTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 23 0.56
49 18 0.44
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (49 bp):
ACCAACTTTCAATGAATTATCTTTTAGTGTTAACTCTAGATGTGAAGGT
Found at i:38200407 original size:26 final size:27
Alignment explanation
Indices: 38200355--38200492 Score: 84
Period size: 27 Copynumber: 5.1 Consensus size: 27
38200345 AGACTATCCA
*
38200355 TTCATAATTCACCATAAAAGCTTTTCT
1 TTCATAATTCACCACAAAAGCTTTTCT
*
38200382 TTCATGATTCACCAC-AAAGAC-TTTCTT
1 TTCATAATTCACCACAAAAG-CTTTTC-T
* * * *
38200409 TTCATATTTCGCTACAAAGGCTTTTCT
1 TTCATAATTCACCACAAAAGCTTTTCT
* * *** * *
38200436 CTT-GTATTTTGTCACAAAGGCTTTCCT
1 -TTCATAATTCACCACAAAAGCTTTTCT
* * *
38200463 TTCATATTTCACCACAAAAACTTTCCT
1 TTCATAATTCACCACAAAAGCTTTTCT
38200490 TTC
1 TTC
38200493 TTGACGTGTT
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
26 10 0.11
27 68 0.78
28 9 0.10
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (27 bp):
TTCATAATTCACCACAAAAGCTTTTCT
Found at i:38201245 original size:2 final size:2
Alignment explanation
Indices: 38201240--38201283 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
38201230 CTTAAAAACA
38201240 AT AT AT 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 AT AT AT
38201282 AT
1 AT
38201284 GAAATTGACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38202004 original size:30 final size:30
Alignment explanation
Indices: 38201932--38202004 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
38201922 TGCAACTAAG
**
38201932 TTAGGGGCTTAATTAAAATTTTTAAAAATT
1 TTAGGGGCTTAATTAAAATCCTTAAAAATT
** * * *
38201962 TTAATGGTTTAATTAAAATCCTTAGAACTT
1 TTAGGGGCTTAATTAAAATCCTTAAAAATT
38201992 TTAGGGGCTTAAT
1 TTAGGGGCTTAAT
38202005 GAGGATCTCC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (30 bp):
TTAGGGGCTTAATTAAAATCCTTAAAAATT
Found at i:38202122 original size:59 final size:62
Alignment explanation
Indices: 38202001--38202123 Score: 164
Period size: 59 Copynumber: 2.0 Consensus size: 62
38201991 TTTAGGGGCT
*
38202001 TAATGAGGATCTCCAAAAAATTTGGAGAGTCTAATTAAAATTATTTTAAAAATTTTAGAAGGC
1 TAATGAGAATCTCCAAAAAATTTGGAGAGTCTAATTAAAA-TATTTTAAAAATTTTAGAAGGC
* * *
38202064 TAATGAGAATTTCTAAAAAA-TT-GAGGGTCTAATTAAAA-ATTTTAAAAATTATTA-AAGGC
1 TAATGAGAATCTCCAAAAAATTTGGAGAGTCTAATTAAAATATTTTAAAAATT-TTAGAAGGC
38202123 T
1 T
38202124 TAACGATAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
59 18 0.33
60 3 0.05
61 15 0.27
62 2 0.04
63 17 0.31
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.34
Consensus pattern (62 bp):
TAATGAGAATCTCCAAAAAATTTGGAGAGTCTAATTAAAATATTTTAAAAATTTTAGAAGGC
Found at i:38205700 original size:16 final size:16
Alignment explanation
Indices: 38205679--38205709 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38205669 TTTGGTTCGC
38205679 TGTAATAGAATAGAGG
1 TGTAATAGAATAGAGG
*
38205695 TGTAATGGAATAGAG
1 TGTAATAGAATAGAG
38205710 TTATTATAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (16 bp):
TGTAATAGAATAGAGG
Found at i:38206028 original size:57 final size:57
Alignment explanation
Indices: 38205897--38206028 Score: 139
Period size: 57 Copynumber: 2.3 Consensus size: 57
38205887 AATAAGATTA
* *
38205897 TTAATAAAAATAATAA-ATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAAT-AAAATAATAATATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* *
38205955 TTAATAAAA-AAT-ATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAA-
1 TTAATAAAATAATAATATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
38206010 TTACTAAAATCATAATATA
1 TTAATAAAATAATAATATA
38206029 TAATAATATA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
55 13 0.21
56 21 0.33
57 24 0.38
58 5 0.08
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (57 bp):
TTAATAAAATAATAATATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:38206290 original size:22 final size:22
Alignment explanation
Indices: 38206265--38206329 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
38206255 AAAATATTTT
38206265 TTTATATGTCATTAATAATTAA
1 TTTATATGTCATTAATAATTAA
38206287 TTTATATGTCATTAATAATTAA
1 TTTATATGTCATTAATAATTAA
38206309 TTTATATGTCATTAATAATTA
1 TTTATATGTCATTAATAATTA
38206330 TTTTTTATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTATATGTCATTAATAATTAA
Found at i:38206513 original size:52 final size:52
Alignment explanation
Indices: 38206457--38206601 Score: 272
Period size: 52 Copynumber: 2.8 Consensus size: 52
38206447 TTTTGTAGTG
*
38206457 TTAATTATAATTTTTAATCAAACAATTTAAGTAATATAAAATAGAACATTGT
1 TTAATTATAATTTTTAATCAAACAATTTAAGTAATATAAAATAAAACATTGT
*
38206509 TTAATTATAATTTTTAATCAAACAATTTAAGTAATATAATATAAAACATTGT
1 TTAATTATAATTTTTAATCAAACAATTTAAGTAATATAAAATAAAACATTGT
38206561 TTAATTATAATTTTTAATCAAACAATTTAAGTAATATAAAA
1 TTAATTATAATTTTTAATCAAACAATTTAAGTAATATAAAA
38206602 CATTGTTTGA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 90 1.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (52 bp):
TTAATTATAATTTTTAATCAAACAATTTAAGTAATATAAAATAAAACATTGT
Found at i:38206532 original size:28 final size:28
Alignment explanation
Indices: 38206501--38206584 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
38206491 TATAAAATAG
38206501 AACATTGTTTAATTATAATTTTTAATCA
1 AACATTGTTTAATTATAATTTTTAATCA
* * * * *
38206529 AACA--ATTTAA--GTAA-TATAATATAA
1 AACATTGTTTAATTATAATTTTTA-ATCA
38206553 AACATTGTTTAATTATAATTTTTAATCA
1 AACATTGTTTAATTATAATTTTTAATCA
38206581 AACA
1 AACA
38206585 ATTTAAGTAA
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 3 0.08
24 10 0.25
26 10 0.25
28 14 0.35
29 3 0.08
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (28 bp):
AACATTGTTTAATTATAATTTTTAATCA
Found at i:38218333 original size:24 final size:24
Alignment explanation
Indices: 38218301--38218350 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
38218291 AAAGGTACAA
*
38218301 TGGATTGAACTTTGAAGATCACAG
1 TGGATTGAACCTTGAAGATCACAG
*
38218325 TGGATTGAACCTTGAAGATTACAG
1 TGGATTGAACCTTGAAGATCACAG
38218349 TG
1 TG
38218351 CGGGCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (24 bp):
TGGATTGAACCTTGAAGATCACAG
Found at i:38219142 original size:45 final size:45
Alignment explanation
Indices: 38218656--38219148 Score: 169
Period size: 44 Copynumber: 11.1 Consensus size: 45
38218646 ATAGATTAAA
* * * *
38218656 GAAGATAGCAAATCTTGTCTTTCTGTACTGGCAGCGAAGCAGA-T
1 GAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGACT
* * * * * * *
38218700 CGAAGACACCAG--CCTGACCTCTCTG-AGTTTGCAGCGGAGCAGACT
1 -GAAGATAACAGATCTTGTCTTC-CTGTA-TTGGCAGCGAAGCAGACT
** * *
38218745 GAAGATAGGAGATCTTGTCTTCCTGTACTGGCAGCAAAGCAGA-T
1 GAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGACT
* * * ** * * *
38218789 CGAAGACACCAG-CCTCATCTTCTTG-AGTTTGCAGCGGAGCAGACT
1 -GAAGATAACAGATCTTGTCTTCCTGTA-TTGGCAGCGAAGCAGACT
* * ** * *
38218834 GAAGATAACATATCTTGTCTTCCTATGCTAGTAGCGAAGCAGA-T
1 GAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGACT
* * * * * *
38218878 CGAAGACACCAG--CCTGACCTCCATG-AGTTTGCAGCGAAGCAGACT
1 -GAAGATAACAGATCTTGTCTTCC-TGTA-TTGGCAGCGAAGCAGACT
* ** * *
38218923 AAAGATAGGAGATCTTGTCTTCCTGTACTAGCAGCGAAGCAGA-T
1 GAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGACT
* * * * ** * * *
38218967 CGAAAACACCAG--CCTCACCTCTCTAAGT-TT-ACAGCGGAGCAGACT
1 -GAAGATAACAGATCTTGTCTTC-CT--GTATTGGCAGCGAAGCAGACT
* *
38219012 GAATATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGA-T
1 GAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGACT
* * * * * * *
38219056 CGAAGACACCAG-CCTCGCCTTCCTG-AGTTTGCAGCGGAGCAGACT
1 -GAAGATAACAGATCTTGTCTTCCTGTA-TTGGCAGCGAAGCAGACT
* * * *
38219101 GAAGATAACAGATCTTGTTTTCCTGTACTGGCAGTGAAGCAGATT
1 GAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGACT
38219146 GAA
1 GAA
38219149 AACACCAGTC
Statistics
Matches: 312, Mismatches: 104, Indels: 64
0.65 0.22 0.13
Matches are distributed among these distances:
43 22 0.07
44 134 0.43
45 133 0.43
46 23 0.07
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23
Consensus pattern (45 bp):
GAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGACT
Found at i:38219142 original size:267 final size:267
Alignment explanation
Indices: 38218657--38219156 Score: 784
Period size: 267 Copynumber: 1.9 Consensus size: 267
38218647 TAGATTAAAG
* * * *
38218657 AAGATAGCAAATCTTGTCTTTCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTGACCTCT
1 AAGATAGCAAATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAAACACCAGCCTCACCTCT
* * *
38218722 CTGAGTTTGCAGCGGAGCAGACTGAAGATAGGAGATCTTGTCTTCCTGTACTGGCAGCAAAGCAG
66 CTAAGTTTACAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCAAAGCAG
* * *
38218787 ATCGAAGACACCAGCCTCATCTTCTTGAGTTTGCAGCGGAGCAGACTGAAGATAACATATCTTGT
131 ATCGAAGACACCAGCCTCACCTTCCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGT
* * *
38218852 CTTCCTATGCTAGTAGCGAAGCAGATCGAAGACACCAGCCTGACCTCCATGAGTTTGCAGCGAAG
196 CTTCCTATACTAGCAGCGAAGCAGATCGAAAACACCAGCCTGACCTCCATGAGTTTGCAGCGAAG
38218917 CAGACTA
261 CAGACTA
* *
38218924 AAGATAGGAGATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAAACACCAGCCTCACCTCT
1 AAGATAGCAAATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAAACACCAGCCTCACCTCT
* * *
38218989 CTAAGTTTACAGCGGAGCAGACTGAATATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAG
66 CTAAGTTTACAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCAAAGCAG
*
38219054 ATCGAAGACACCAGCCTCGCCTTCCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGT
131 ATCGAAGACACCAGCCTCACCTTCCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGT
* * * * *
38219119 TTTCCTGTACTGGCAGTGAAGCAGATTGAAAACACCAG
196 CTTCCTATACTAGCAGCGAAGCAGATCGAAAACACCAG
38219157 TCTTACCTTT
Statistics
Matches: 209, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
267 209 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (267 bp):
AAGATAGCAAATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAAACACCAGCCTCACCTCT
CTAAGTTTACAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCAAAGCAG
ATCGAAGACACCAGCCTCACCTTCCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGT
CTTCCTATACTAGCAGCGAAGCAGATCGAAAACACCAGCCTGACCTCCATGAGTTTGCAGCGAAG
CAGACTA
Found at i:38219195 original size:89 final size:89
Alignment explanation
Indices: 38218656--38219178 Score: 699
Period size: 89 Copynumber: 5.9 Consensus size: 89
38218646 ATAGATTAAA
* * * *
38218656 GAAGATAGCAAATCTTGTCTTTCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTGACCTC
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTCACCTT
38218721 TCTGAGTTTGCAGCGGAGCAGACT
66 TCTGAGTTTGCAGCGGAGCAGACT
* * *
38218745 GAAGATAGGAGATCTTGTCTTCCTGTACTGGCAGCAAAGCAGATCGAAGACACCAGCCTCATC-T
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTCACCTT
38218809 TCTTGAGTTTGCAGCGGAGCAGACT
66 TC-TGAGTTTGCAGCGGAGCAGACT
* * * * * * *
38218834 GAAGATAACATATCTTGTCTTCCTATGCTAGTAGCGAAGCAGATCGAAGACACCAGCCTGACC-T
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTCACCTT
* *
38218898 CCATGAGTTTGCAGCGAAGCAGACT
66 TC-TGAGTTTGCAGCGGAGCAGACT
* * * * *
38218923 AAAGATAGGAGATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAAACACCAGCCTCACCTC
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTCACCTT
* *
38218988 TCTAAGTTTACAGCGGAGCAGACT
66 TCTGAGTTTGCAGCGGAGCAGACT
* * *
38219012 GAATATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTCGCCTT
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTCACCTT
*
38219077 CCTGAGTTTGCAGCGGAGCAGACT
66 TCTGAGTTTGCAGCGGAGCAGACT
* * * * * * *
38219101 GAAGATAACAGATCTTGTTTTCCTGTACTGGCAGTGAAGCAGATTGAAAACACCAGTCTTACCTT
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTCACCTT
*
38219166 TCTAAGTTTGCAG
66 TCTGAGTTTGCAG
38219179 TAGAGTAGGT
Statistics
Matches: 375, Mismatches: 57, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
88 2 0.01
89 372 0.99
90 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (89 bp):
GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTCACCTT
TCTGAGTTTGCAGCGGAGCAGACT
Found at i:38221353 original size:4 final size:4
Alignment explanation
Indices: 38221337--38221367 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
38221327 AATATATTTT
38221337 TTTC TTT- TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
38221368 AATAATCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:38224884 original size:21 final size:21
Alignment explanation
Indices: 38224860--38224907 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
38224850 CGACTGTGGC
* *
38224860 GGAGGACTAGCAGCTGGGGGT
1 GGAGGACTAACAGCTGAGGGT
*
38224881 GGAGGACTAACAGGTGAGGGT
1 GGAGGACTAACAGCTGAGGGT
38224902 GGAGGA
1 GGAGGA
38224908 GACAAGGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.52, T:0.12
Consensus pattern (21 bp):
GGAGGACTAACAGCTGAGGGT
Found at i:38235759 original size:41 final size:41
Alignment explanation
Indices: 38235692--38235804 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
38235682 TTAATTTAAA
* * *
38235692 CAGATTCAACGGCACTTAGCCT-CTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
38235733 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
38235774 CAGATCACCGGCACGTAGCCTGCTAGACTTA
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTA
38235805 AAGTCTGAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 15 0.23
41 50 0.77
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (41 bp):
CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
Found at i:38246666 original size:20 final size:20
Alignment explanation
Indices: 38246636--38246686 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
38246626 ATCCACATAT
*
38246636 AATTCATAAAAAT-TTAAAA
1 AATTAATAAAAATATTAAAA
38246655 ATATTAATAAAAATATTAAAA
1 A-ATTAATAAAAATATTAAAA
38246676 AATTAA-AAAAA
1 AATTAATAAAAA
38246687 GTTCATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.21
20 16 0.55
21 7 0.24
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AATTAATAAAAATATTAAAA
Found at i:38249465 original size:21 final size:21
Alignment explanation
Indices: 38249441--38249488 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
38249431 CGACTGTGGC
* *
38249441 GGAGGACTAGCAGCTGGGGGT
1 GGAGGACTAACAGCTGAGGGT
*
38249462 GGAGGACTAACAGGTGAGGGT
1 GGAGGACTAACAGCTGAGGGT
38249483 GGAGGA
1 GGAGGA
38249489 TATAAGGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.52, T:0.12
Consensus pattern (21 bp):
GGAGGACTAACAGCTGAGGGT
Found at i:38250714 original size:24 final size:24
Alignment explanation
Indices: 38250679--38250730 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
38250669 ATTGTGACCC
38250679 TTTTTTTAATTTGTGAGATT-T-AAA
1 TTTTTTTAATTT-T-AGATTATCAAA
*
38250703 TTTTTTTTATTTTAGATTATCAAA
1 TTTTTTTAATTTTAGATTATCAAA
38250727 TTTT
1 TTTT
38250731 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 2 0.08
24 18 0.72
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (24 bp):
TTTTTTTAATTTTAGATTATCAAA
Found at i:38261363 original size:27 final size:27
Alignment explanation
Indices: 38261333--38261471 Score: 93
Period size: 27 Copynumber: 5.1 Consensus size: 27
38261323 AGGCTATCCA
* *
38261333 TTCATAATTCACCATAAAG-CTTTTTCT
1 TTCATAATTCACCACAAAGACTTTCT-T
*
38261360 TTCATGATTCACCACAAAGACTTTCTT
1 TTCATAATTCACCACAAAGACTTTCTT
* * * *
38261387 TTCATATTTGACTACAAAAGGCTTT-TCT
1 TTCATAATTCACCAC-AAAGACTTTCT-T
* * *** * *
38261415 CTCATATTTTGTCACAAAGGCTTTCCT
1 TTCATAATTCACCACAAAGACTTTCTT
* *
38261442 TTCATATTTCACCACAAAGACTTTCAT
1 TTCATAATTCACCACAAAGACTTTCTT
38261469 TTC
1 TTC
38261472 CTGACGTGTT
Statistics
Matches: 88, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
27 64 0.73
28 24 0.27
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (27 bp):
TTCATAATTCACCACAAAGACTTTCTT
Found at i:38262174 original size:17 final size:16
Alignment explanation
Indices: 38262152--38262186 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
38262142 ATAAAATTTT
*
38262152 AAAAAAACAGAAAATAG
1 AAAAAAAAAGAAAA-AG
38262169 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
38262185 AA
1 AA
38262187 TACAAACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:38263895 original size:19 final size:19
Alignment explanation
Indices: 38263847--38263893 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
38263837 TGACAACCCA
38263847 TTTTCAAAATTTTCAATTT
1 TTTTCAAAATTTTCAATTT
**
38263866 TTTTCAAAATTTTCTGTTT
1 TTTTCAAAATTTTCAATTT
38263885 TGTTTCAAA
1 T-TTTCAAA
38263894 TTGATCCCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTTCAAAATTTTCAATTT
Found at i:38274278 original size:12 final size:12
Alignment explanation
Indices: 38274263--38274294 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
38274253 TAATGAAAAT
38274263 ATAAATAAAGAA
1 ATAAATAAAGAA
38274275 ATAAATAAAGAA
1 ATAAATAAAGAA
*
38274287 ATGAATAA
1 ATAAATAA
38274295 GGCTATAAAA
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:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (12 bp):
ATAAATAAAGAA
Found at i:38274369 original size:16 final size:16
Alignment explanation
Indices: 38274348--38274386 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
38274338 AATTATGGAG
*
38274348 ATATATGAAAGCATGT
1 ATATATAAAAGCATGT
*
38274364 ATATATAAAAGTATGT
1 ATATATAAAAGCATGT
38274380 ATATATA
1 ATATATA
38274387 TGTATACTTT
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:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (16 bp):
ATATATAAAAGCATGT
Found at i:38277580 original size:21 final size:21
Alignment explanation
Indices: 38277551--38277594 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
38277541 GGTTGGTTGG
* *
38277551 TTTAGGGTTAATTGGGTCTGGT
1 TTTAGGGTT-AGTGGGCCTGGT
38277573 TTTA-GGTTAGTGGGCCTGGT
1 TTTAGGGTTAGTGGGCCTGGT
38277593 TT
1 TT
38277595 GATTTGGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 4 0.20
22 4 0.20
ACGTcount: A:0.11, C:0.07, G:0.36, T:0.45
Consensus pattern (21 bp):
TTTAGGGTTAGTGGGCCTGGT
Found at i:38278382 original size:172 final size:172
Alignment explanation
Indices: 38278092--38278421 Score: 414
Period size: 172 Copynumber: 1.9 Consensus size: 172
38278082 CAATCTTTTA
* * * *
38278092 ATTGCAATGTTGGGAAAGCAAGATTCGCCATTGTGGCTTCAATCTATTCCATTACATCGCCAGGG
1 ATTGCAATGTCGGGAAAGCAAGATTCGCCATTGTAGCTTCAATCTATTCCACTACATCACCAGGG
* * * *
38278157 AAGTAAGATTTGCTGTTGTAGCTTCAATCTATTTGACTACAATGTCGGGGAAGCGAGATTCAC-C
66 AAGTAAGATTCGCTGTTGTAGCCTCAATCTATTTAACTACAATGTCAGGGAAGCGAGATTC-CTC
*
38278221 ATCGTAGCTTCAATTTGTTCCACTGCACCCCTAGAGAAATGAG
130 ATCGTAGCTTCAATCTGTTCCACTGCACCCCTAGAGAAATGAG
* * * * * *
38278264 ATTGCAATGTCGGGGAAGGAAGATTTGCCGTTGTAGCTTCAATCTATTCCACTGCATCACCTGGG
1 ATTGCAATGTCGGGAAAGCAAGATTCGCCATTGTAGCTTCAATCTATTCCACTACATCACCAGGG
* * * *
38278329 AAGGTAAGATTCG-TCGTTGTGGCCTCAATCT-TTTAATTGCAATGTTAGGGAAGCGAGATTCCT
66 AA-GTAAGATTCGCT-GTTGTAGCCTCAATCTATTTAACTACAATGTCAGGGAAGCGAGATTCCT
* * *
38278392 CGTTGTGGCTTCAATCTGTTCCACTGCACC
129 CATCGTAGCTTCAATCTGTTCCACTGCACC
38278422 ACCTGGGAAA
Statistics
Matches: 133, Mismatches: 22, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
171 1 0.01
172 109 0.82
173 23 0.17
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (172 bp):
ATTGCAATGTCGGGAAAGCAAGATTCGCCATTGTAGCTTCAATCTATTCCACTACATCACCAGGG
AAGTAAGATTCGCTGTTGTAGCCTCAATCTATTTAACTACAATGTCAGGGAAGCGAGATTCCTCA
TCGTAGCTTCAATCTGTTCCACTGCACCCCTAGAGAAATGAG
Found at i:38278397 original size:49 final size:49
Alignment explanation
Indices: 38278325--38278967 Score: 269
Period size: 49 Copynumber: 12.9 Consensus size: 49
38278315 CTGCATCACC
*
38278325 TGGGAAGGTAAGATTC-GTCGTTGTGGCCTCAATCTTTTAATTGCAATGT
1 TGGGAA-GTAAGATTCACTCGTTGTGGCCTCAATCTTTTAATTGCAATGT
** * ** * **
38278374 TAGGGAAGCGAGATTC-CTCGTTGTGGCTTCAATCTGTTCCACTGCACCA-CC
1 T-GGGAAGTAAGATTCACTCGTTGTGGCCTCAATCT-TTTAATTGCA--ATGT
*
38278425 TGGGAAAGTAAGATTCAC-CATTGTGGCCTCAATCTTTTAATTGCAATGT
1 TGGG-AAGTAAGATTCACTCGTTGTGGCCTCAATCTTTTAATTGCAATGT
* * * * * * *
38278474 TGGGGAAGTAAGATTCACT-ATTGTAGCTTCAATCTGTTCAACTGCACTGCC
1 T-GGGAAGTAAGATTCACTCGTTGTGGCCTCAATCT-TTTAATTGCAATG-T
* * * *
38278525 TGTGAAATAAGATTCGC-CGTTGTGGCCTCAATCCTTTAATTGCAATGT
1 TGGGAAGTAAGATTCACTCGTTGTGGCCTCAATCTTTTAATTGCAATGT
* * * * * * * * * *
38278573 CAGGGAAGCAAGATTCGCT-GTTGTAGCTTCAATCTGTTCAACTGTACTGCC
1 -TGGGAAGTAAGATTCACTCGTTGTGGCCTCAATCT-TTTAATTGCAATG-T
* * * ** *
38278624 TGGGAAATAAGATTCGC-CATTGTGGTTTCAATCTTTTAATTACAATGT
1 TGGGAAGTAAGATTCACTCGTTGTGGCCTCAATCTTTTAATTGCAATGT
* * * * * * * * * *
38278672 CGGGGAAGCAAGATTCGCT-ATTTTAGCTTCAATCTGTTCAATTGCACTGCC
1 -TGGGAAGTAAGATTCACTCGTTGTGGCCTCAATCT-TTTAATTGCAATG-T
* * * * *
38278723 TGGGAAATAAGATTCGC-CGTTGTGGCTTCAATCTTTTGATTGCAATAT
1 TGGGAAGTAAGATTCACTCGTTGTGGCCTCAATCTTTTAATTGCAATGT
* ** * * * * **
38278771 CGGGGAAGCGAGATTCGC-CGTTGTGGCTTCAAT-TTGTTCCACTGCACCA-CC
1 -TGGGAAGTAAGATTCACTCGTTGTGGCCTCAATCTT-TT-AATTGCA--ATGT
*
38278822 TGGGAAAGTAAGATTCGC-CGTTGTGGCCTCAATCTTTTAATTGCAATGT
1 TGGG-AAGTAAGATTCACTCGTTGTGGCCTCAATCTTTTAATTGCAATGT
** * * * * *
38278871 CAAGGAA-TCAAGATTCACT-GTTGTAGCTTCAATCTGTTCAACTGC-ATCGCC
1 -TGGGAAGT-AAGATTCACTCGTTGTGGCCTCAATCT-TTTAATTGCAAT-G-T
* * *
38278922 TAGGAAGTAAGATTCAC-CGTTGTGGCTTTAATCTTTTGAATTGCAA
1 TGGGAAGTAAGATTCACTCGTTGTGGCCTCAATCTTTT-AATTGCAA
38278968 ACTATGGTTT
Statistics
Matches: 445, Mismatches: 109, Indels: 78
0.70 0.17 0.12
Matches are distributed among these distances:
48 5 0.01
49 191 0.43
50 189 0.42
51 55 0.12
52 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (49 bp):
TGGGAAGTAAGATTCACTCGTTGTGGCCTCAATCTTTTAATTGCAATGT
Found at i:38278437 original size:100 final size:100
Alignment explanation
Indices: 38278264--38278967 Score: 869
Period size: 99 Copynumber: 7.1 Consensus size: 100
38278254 GAGAAATGAG
* * * * * * * *
38278264 ATTGCAATGTCGGGGAAGGAAGATTTGCCGTTGTAGCTTCAATCTATTCCACTGCATCACCTGGG
1 ATTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCAACTGCACCGCCTGGG
* *
38278329 AAGGTAAGATTCGTCGTTGTGGCCTCAATCTTTTA
66 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTA
* * * * *
38278364 ATTGCAATGTTAGGGAAGCGAGATTC-CTCGTTGTGGCTTCAATCTGTTCCACTGCACCACCTGG
1 ATTGCAATGTCAGGGAAGCAAGATTCGCT-GTTGTAGCTTCAATCTGTTCAACTGCACCGCCTGG
* *
38278428 GAAAGTAAGATTCACCATTGTGGCCTCAATCTTTTA
65 GAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTA
** * * * * *
38278464 ATTGCAATGTTGGGGAAGTAAGATTCACTATTGTAGCTTCAATCTGTTCAACTGCACTGCCTGTG
1 ATTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCAACTGCACCGCCTGGG
*
38278529 AAA-TAAGATTCGCCGTTGTGGCCTCAATCCTTTA
66 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTA
* *
38278563 ATTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCAACTGTACTGCCTGGG
1 ATTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCAACTGCACCGCCTGGG
* **
38278628 AAA-TAAGATTCGCCATTGTGGTTTCAATCTTTTA
66 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTA
* * * * * *
38278662 ATTACAATGTCGGGGAAGCAAGATTCGCTATTTTAGCTTCAATCTGTTCAATTGCACTGCCTGGG
1 ATTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCAACTGCACCGCCTGGG
* *
38278727 AAA-TAAGATTCGCCGTTGTGGCTTCAATCTTTTG
66 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTA
* * * * * * * *
38278761 ATTGCAATATCGGGGAAGCGAGATTCGCCGTTGTGGCTTCAATTTGTTCCACTGCACCACCTGGG
1 ATTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCAACTGCACCGCCTGGG
38278826 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTA
66 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTA
* * * * *
38278861 ATTGCAATGTCAAGGAATCAAGATTCACTGTTGTAGCTTCAATCTGTTCAACTGCATCGCCTAGG
1 ATTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCAACTGCACCGCCTGGG
* * *
38278926 -AAGTAAGATTCACCGTTGTGGCTTTAATCTTTTGA
66 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTT-A
38278961 ATTGCAA
1 ATTGCAA
38278968 ACTATGGTTT
Statistics
Matches: 525, Mismatches: 75, Indels: 8
0.86 0.12 0.01
Matches are distributed among these distances:
99 293 0.56
100 230 0.44
101 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (100 bp):
ATTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCAACTGCACCGCCTGGG
AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTA
Found at i:38278654 original size:50 final size:50
Alignment explanation
Indices: 38278394--38278955 Score: 359
Period size: 50 Copynumber: 11.3 Consensus size: 50
38278384 AGATTCCTCG
* ** *
38278394 TTGTGGCTTCAATCTGTTCCACTGCACCACCTGGGAAAGTAAGATTCACCA
1 TTGTGGCTTCAATCTGTTCAACTGCACTGCCTGGGAAA-TAAGATTCGCCA
* * * * * * * *
38278445 TTGTGGCCTCAATCT-TTTAATTGCAATG-TTGGGGAAGTAAGATTCACTA
1 TTGTGGCTTCAATCTGTTCAACTGCACTGCCT-GGGAAATAAGATTCGCCA
* * *
38278494 TTGTAGCTTCAATCTGTTCAACTGCACTGCCTGTGAAATAAGATTCGCCG
1 TTGTGGCTTCAATCTGTTCAACTGCACTGCCTGGGAAATAAGATTCGCCA
* * * * * ** **
38278544 TTGTGGCCTCAATCCT-TT-AATTGCAATGTCAGGGAAGCAAGATTCGCTG
1 TTGTGGCTTCAAT-CTGTTCAACTGCACTGCCTGGGAAATAAGATTCGCCA
* *
38278593 TTGTAGCTTCAATCTGTTCAACTGTACTGCCTGGGAAATAAGATTCGCCA
1 TTGTGGCTTCAATCTGTTCAACTGCACTGCCTGGGAAATAAGATTCGCCA
* * * * * * * ** *
38278643 TTGTGGTTTCAATCT-TTTAATTACAATGTCGGGGAAGCAAGATTCGCTA
1 TTGTGGCTTCAATCTGTTCAACTGCACTGCCTGGGAAATAAGATTCGCCA
* * * *
38278692 TTTTAGCTTCAATCTGTTCAATTGCACTGCCTGGGAAATAAGATTCGCCG
1 TTGTGGCTTCAATCTGTTCAACTGCACTGCCTGGGAAATAAGATTCGCCA
** * * ** * *** *
38278742 TTGTGGCTTCAATCT-TTTGATTGCAATATCGGGGAAGCGAGATTCGCCG
1 TTGTGGCTTCAATCTGTTCAACTGCACTGCCTGGGAAATAAGATTCGCCA
* * ** *
38278791 TTGTGGCTTCAATTTGTTCCACTGCACCACCTGGGAAAGTAAGATTCGCCG
1 TTGTGGCTTCAATCTGTTCAACTGCACTGCCTGGGAAA-TAAGATTCGCCA
* * * * * ** * **
38278842 TTGTGGCCTCAATCT-TTTAATTGCAATGTCAAGG-AATCAAGATTCACTG
1 TTGTGGCTTCAATCTGTTCAACTGCACTGCCTGGGAAAT-AAGATTCGCCA
* * * * *
38278891 TTGTAGCTTCAATCTGTTCAACTGCA-TCGCCTAGGAAGTAAGATTCACCG
1 TTGTGGCTTCAATCTGTTCAACTGCACT-GCCTGGGAAATAAGATTCGCCA
*
38278941 TTGTGGCTTTAATCT
1 TTGTGGCTTCAATCT
38278956 TTTGAATTGC
Statistics
Matches: 387, Mismatches: 111, Indels: 27
0.74 0.21 0.05
Matches are distributed among these distances:
48 3 0.01
49 161 0.42
50 181 0.47
51 42 0.11
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (50 bp):
TTGTGGCTTCAATCTGTTCAACTGCACTGCCTGGGAAATAAGATTCGCCA
Found at i:38280139 original size:21 final size:21
Alignment explanation
Indices: 38280113--38280159 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
38280103 GGTATAGCAA
38280113 GATCACCACATGCCCCAATCT
1 GATCACCACATGCCCCAATCT
** *
38280134 GATCACTTCATGCCCCATTCT
1 GATCACCACATGCCCCAATCT
38280155 GATCA
1 GATCA
38280160 ATTTTGAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.38, G:0.11, T:0.26
Consensus pattern (21 bp):
GATCACCACATGCCCCAATCT
Found at i:38280264 original size:15 final size:14
Alignment explanation
Indices: 38280243--38280293 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
38280233 TTAGCCTCTC
38280243 CATTTTT-ACTTTTT
1 CATTTTTCA-TTTTT
38280257 CAATTTTTCATTTTT
1 C-ATTTTTCATTTTT
**
38280272 CATTTTTTTTATTTT
1 CATTTTTCAT-TTTT
38280287 CATTTTT
1 CATTTTT
38280294 TTGTTTGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 8 0.25
15 23 0.72
16 1 0.03
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.73
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:38280268 original size:22 final size:22
Alignment explanation
Indices: 38280243--38280293 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
38280233 TTAGCCTCTC
38280243 CATTTTT-ACTTTTTCAATTTTT
1 CATTTTTCACTTTTTCAA-TTTT
* **
38280265 CATTTTTCATTTTTTTTATTTT
1 CATTTTTCACTTTTTCAATTTT
38280287 CATTTTT
1 CATTTTT
38280294 TTGTTTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.73
Consensus pattern (22 bp):
CATTTTTCACTTTTTCAATTTT
Found at i:38280278 original size:7 final size:7
Alignment explanation
Indices: 38280243--38280293 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
38280233 TTAGCCTCTC
38280243 CATTTTT
1 CATTTTT
38280250 -ACTTTTT
1 CA-TTTTT
38280257 CAATTTTT
1 C-ATTTTT
38280265 CATTTTT
1 CATTTTT
38280272 CATTTTT
1 CATTTTT
**
38280279 TTTATTTT
1 CAT-TTTT
38280287 CATTTTT
1 CATTTTT
38280294 TTGTTTGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
6 1 0.03
7 23 0.64
8 11 0.31
9 1 0.03
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
CATTTTT
Found at i:38283766 original size:19 final size:19
Alignment explanation
Indices: 38283719--38283766 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
38283709 CACTTTGTGA
* *
38283719 AAATCTAATGCATATGATG
1 AAATGTAATGCAAATGATG
*
38283738 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATG-ATG
38283758 AAATG-AATG
1 AAATGTAATG
38283767 TAAAAAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (19 bp):
AAATGTAATGCAAATGATG
Found at i:38285704 original size:12 final size:12
Alignment explanation
Indices: 38285689--38285720 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
38285679 TAATGAAAAT
38285689 ATAAATAAAGAA
1 ATAAATAAAGAA
38285701 ATAAATAAAGAA
1 ATAAATAAAGAA
*
38285713 ATGAATAA
1 ATAAATAA
38285721 GGCTATAAAA
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:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (12 bp):
ATAAATAAAGAA
Found at i:38285795 original size:16 final size:16
Alignment explanation
Indices: 38285774--38285812 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
38285764 AATTATGGAG
*
38285774 ATATATGAAAGCATGT
1 ATATATAAAAGCATGT
*
38285790 ATATATAAAAGTATGT
1 ATATATAAAAGCATGT
38285806 ATATATA
1 ATATATA
38285813 TGTATACTTT
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:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (16 bp):
ATATATAAAAGCATGT
Found at i:38285861 original size:49 final size:49
Alignment explanation
Indices: 38285800--38285917 Score: 193
Period size: 49 Copynumber: 2.4 Consensus size: 49
38285790 ATATATAAAA
*
38285800 GTATGTATATATATGTATACTTTATATATTTATGTAAAAAAAGAACAAT
1 GTATATATATATATGTATACTTTATATATTTATGTAAAAAAAGAACAAT
38285849 GTATATATATATATGTATACTTTATATATTTATGTAAAAAAAGAACAAT
1 GTATATATATATATGTATACTTTATATATTTATGTAAAAAAAGAACAAT
*
38285898 GTACGTATAAATATAT-TATA
1 GTA--TATATATATATGTATA
38285918 TAAATGAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
49 51 0.78
50 4 0.06
51 10 0.15
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (49 bp):
GTATATATATATATGTATACTTTATATATTTATGTAAAAAAAGAACAAT
Found at i:38288681 original size:21 final size:21
Alignment explanation
Indices: 38288655--38288702 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
38288645 CGACTATGGC
* *
38288655 GGAGGACTAGCAGCTGGGGGT
1 GGAGGACTAACAGCTGAGGGT
*
38288676 GGAGGACTAACAGGTGAGGGT
1 GGAGGACTAACAGCTGAGGGT
38288697 GGAGGA
1 GGAGGA
38288703 GACAAGGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.52, T:0.12
Consensus pattern (21 bp):
GGAGGACTAACAGCTGAGGGT
Found at i:38289692 original size:5 final size:5
Alignment explanation
Indices: 38289682--38289713 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
38289672 GAATTTAAAC
38289682 TATTT TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TATTT TA
38289714 AGTTAATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:38290178 original size:25 final size:26
Alignment explanation
Indices: 38290136--38290185 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
38290126 AATAAGATGT
* *
38290136 ATTTAATTTTTTTTTTTTAAATTTAA
1 ATTTAATTTATTTATTTTAAATTTAA
*
38290162 ATTT-ATTTATTTATTTTAATTTTA
1 ATTTAATTTATTTATTTTAAATTTA
38290186 TACATATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
ATTTAATTTATTTATTTTAAATTTAA
Found at i:38291642 original size:4 final size:4
Alignment explanation
Indices: 38291633--38291659 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
38291623 ATTACATATT
38291633 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
38291660 TGGTATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:38292038 original size:11 final size:11
Alignment explanation
Indices: 38292022--38292128 Score: 72
Period size: 11 Copynumber: 10.4 Consensus size: 11
38292012 ATTTTTTTAA
38292022 TTTTAAAATAT
1 TTTTAAAATAT
38292033 TTTTAAAATACT
1 TTTTAAAATA-T
**
38292045 TTTTTTAAT-T
1 TTTTAAAATAT
38292055 TTTT--AA-A-
1 TTTTAAAATAT
38292062 TTTTAAAATAT
1 TTTTAAAATAT
38292073 TTTTAAAATACT
1 TTTTAAAATA-T
*
38292085 TTTT-TAAT-T
1 TTTTAAAATAT
* *
38292094 TTTT---TTAA
1 TTTTAAAATAT
38292102 TTTTAAAATAT
1 TTTTAAAATAT
38292113 TTTTAAAATACT
1 TTTTAAAATA-T
38292125 TTTT
1 TTTT
38292129 TTAATTTTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
7 5 0.06
8 6 0.08
9 7 0.09
10 6 0.08
11 35 0.45
12 18 0.23
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:38292048 original size:31 final size:28
Alignment explanation
Indices: 38292010--38292142 Score: 100
Period size: 31 Copynumber: 4.8 Consensus size: 28
38292000 TAATAAATAT
38292010 ATATTTTTTTAATTTTAAAATATTTTTAAA
1 ATATTTTTTTAATTTTAAAA-A-TTTTAAA
**
38292040 ATACTTTTTTTAATTTTTTAAATTTTAAA
1 ATA-TTTTTTTAATTTTAAAAATTTTAAA
* * **
38292069 ATA--TTTTTAA----AATACTTTTTTA
1 ATATTTTTTTAATTTTAAAAATTTTAAA
38292091 AT-TTTTTTTAATTTTAAAATATTTTTAAA
1 ATATTTTTTTAATTTTAAAA-A-TTTTAAA
*
38292120 ATACTTTTTTTAATTTTTAAAAT
1 ATA-TTTTTTTAATTTTAAAAAT
38292143 AAATTTTTAG
Statistics
Matches: 79, Mismatches: 13, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
22 8 0.10
23 7 0.09
26 7 0.09
27 3 0.04
29 18 0.23
30 5 0.06
31 31 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
ATATTTTTTTAATTTTAAAAATTTTAAA
Found at i:38292057 original size:40 final size:40
Alignment explanation
Indices: 38292012--38292137 Score: 227
Period size: 40 Copynumber: 3.1 Consensus size: 40
38292002 ATAAATATAT
38292012 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
*
38292052 ATTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
38292091 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 A-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
38292132 ATTTTT
1 ATTTTT
38292138 AAAATAAATT
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
39 8 0.10
40 66 0.80
41 8 0.10
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:38292149 original size:21 final size:21
Alignment explanation
Indices: 38292111--38292150 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38292101 ATTTTAAAAT
**
38292111 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
38292132 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
38292151 AGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:38292157 original size:22 final size:21
Alignment explanation
Indices: 38292110--38292168 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
38292100 AATTTTAAAA
* *
38292110 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
38292130 TAATTTTTAAAATAAATTTTTAG
1 T-ATTTTTAAAATAAATTTTT-G
38292153 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
38292169 GGGCCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:38293594 original size:14 final size:14
Alignment explanation
Indices: 38293575--38293614 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
38293565 TTGTTTGCCA
38293575 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
38293589 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
38293603 GGAAAATGTTTT
1 GTAAAATGTTTT
38293615 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:38293621 original size:34 final size:35
Alignment explanation
Indices: 38293583--38293649 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
38293573 CAGTAAAATG
*
38293583 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
38293617 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
38293650 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:38293623 original size:20 final size:20
Alignment explanation
Indices: 38293598--38293637 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38293588 CGTAAAATGA
*
38293598 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
38293618 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
38293638 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:38293653 original size:14 final size:15
Alignment explanation
Indices: 38293577--38293653 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
38293567 GTTTGCCAGT
* *
38293577 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
38293591 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
38293605 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
38293625 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
38293640 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
38293654 TGTTTGGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:38293714 original size:32 final size:32
Alignment explanation
Indices: 38293628--38293715 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 32
38293618 TTTCTGTAAA
* *
38293628 ATGATTTACTGGAAAATATTTTCTGGTGTTTGG
1 ATGATTTCCT-GAAAATATTTTCTGCTGTTTGG
* *
38293661 ATGA-ATCTGTGTAAAATATTTTCTGCTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGCTGTTTGG
38293694 -TAGATTTCCTGAAAATATTTTC
1 AT-GATTTCCTGAAAATATTTTC
38293716 CGGAAAAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
32 14 0.31
33 29 0.64
34 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.45
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGCTGTTTGG
Found at i:38304409 original size:15 final size:15
Alignment explanation
Indices: 38304391--38304425 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
38304381 TGGTTTAAAT
38304391 TTATATATTATCATC
1 TTATATATTATCATC
*
38304406 TTATATATTATTATC
1 TTATATATTATCATC
38304421 -TATAT
1 TTATAT
38304426 TAAAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATATTATCATC
Found at i:38305244 original size:115 final size:115
Alignment explanation
Indices: 38305075--38305284 Score: 330
Period size: 115 Copynumber: 1.8 Consensus size: 115
38305065 AAGGAAAATT
* * * * * *
38305075 TTTCAAAATGAGGTAATGTTTTGCTTTTGGAAAATCGAGAAAATGTGCTCTAACGTGCTGGGTTT
1 TTTCAAAACGAGGCAATGTTTTGCGTTTGGAAAATCAAGAAAACGTGCCCTAACGTGCTGGGTTT
38305140 CGATTTCTCGTTCGACCAAATAGCCAAATAGCCAAATATCCTTTCAATAA
66 CGATTTCTCGTTCGACCAAATAGCCAAATAGCCAAATATCCTTTCAATAA
* *
38305190 TTTCAAAACGAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACGTGCCCTAACGTGCTGTGTTT
1 TTTCAAAACGAGGCAATGTTTTGCGTTTGGAAAATCAAGAAAACGTGCCCTAACGTGCTGGGTTT
* *
38305255 TGATTTCTCGTTCGACTAAATAGCCAAATA
66 CGATTTCTCGTTCGACCAAATAGCCAAATA
38305285 TCCTCTTAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
115 85 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (115 bp):
TTTCAAAACGAGGCAATGTTTTGCGTTTGGAAAATCAAGAAAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCGTTCGACCAAATAGCCAAATAGCCAAATATCCTTTCAATAA
Found at i:38311274 original size:15 final size:15
Alignment explanation
Indices: 38311254--38311282 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38311244 ATTTCAAATA
38311254 ATCAGAAAAAAAAGT
1 ATCAGAAAAAAAAGT
38311269 ATCAGAAAAAAAAG
1 ATCAGAAAAAAAAG
38311283 AGAGAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (15 bp):
ATCAGAAAAAAAAGT
Found at i:38315183 original size:19 final size:18
Alignment explanation
Indices: 38315156--38315193 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
38315146 AAATTCACAT
*
38315156 ATTTTAATAATTTTAAAAA
1 ATTTAAATAA-TTTAAAAA
38315175 ATTTAAATAATTTAAAAA
1 ATTTAAATAATTTAAAAA
38315193 A
1 A
38315194 CTTCTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAATAATTTAAAAA
Found at i:38315326 original size:21 final size:21
Alignment explanation
Indices: 38315302--38315350 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
38315292 CACTGTTTCT
*
38315302 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
38315323 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
38315344 AATCTCA
1 AATCTCA
38315351 TCGCCACCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.35, G:0.08, T:0.24
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:38319679 original size:16 final size:15
Alignment explanation
Indices: 38319658--38319688 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
38319648 TATAAAAATA
38319658 TTAATTAACTTAATTT
1 TTAATTAA-TTAATTT
38319674 TTAATTAATTAATTT
1 TTAATTAATTAATTT
38319689 AGTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTAATTAATTT
Found at i:38321346 original size:15 final size:15
Alignment explanation
Indices: 38321321--38321355 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
38321311 AACTCTATTT
*
38321321 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
38321335 TAATTAATATTAAGA
1 TAATTAATATTAAGA
38321350 TAATTA
1 TAATTA
38321356 TTAAGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:38325206 original size:4 final size:4
Alignment explanation
Indices: 38325193--38325260 Score: 61
Period size: 4 Copynumber: 16.5 Consensus size: 4
38325183 CAACTCAATT
*
38325193 TTTA -TTA TTTA TTTA TTTA TTTA TTTTC TTTA CTTTA TTTA -TTA CTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA TTTA TTTA -TTTA
38325242 TTTTA TTT- TATTA TTTA TT
1 -TTTA TTTA T-TTA TTTA TT
38325261 ACTTATTTGG
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
3 7 0.13
4 32 0.59
5 15 0.28
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:38325232 original size:22 final size:21
Alignment explanation
Indices: 38325197--38325260 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
38325187 TCAATTTTTA
38325197 TTATTTATTTATTTATTTATT
1 TTATTTATTTATTTATTTATT
* *
38325218 TTCTTTACTTTATTTA-TTACT
1 TTATTTA-TTTATTTATTTATT
38325239 TTATTTTATTT-TATTATTTATT
1 TTA-TTTATTTAT-TTATTTATT
38325261 ACTTATTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.03
21 18 0.51
22 16 0.46
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATTTATTTATTTATTTATT
Found at i:38326912 original size:15 final size:15
Alignment explanation
Indices: 38326887--38326921 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
38326877 AACTCTATTT
*
38326887 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
38326901 TAATTAATATTAAGA
1 TAATTAATATTAAGA
38326916 TAATTA
1 TAATTA
38326922 TTAAGATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:38328534 original size:15 final size:15
Alignment explanation
Indices: 38328514--38328542 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38328504 AGGAGGTGGA
38328514 GGAGATAAGGATGGC
1 GGAGATAAGGATGGC
38328529 GGAGATAAGGATGG
1 GGAGATAAGGATGG
38328543 GGCTGCAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.48, T:0.14
Consensus pattern (15 bp):
GGAGATAAGGATGGC
Found at i:38331882 original size:22 final size:22
Alignment explanation
Indices: 38331857--38331900 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38331847 AACCCAAAAT
38331857 CAAAGCAAAC-AAACTTAAACCC
1 CAAAGCAAACTAAA-TTAAACCC
*
38331879 CAAAGCCAACTAAATTAAACCC
1 CAAAGCAAACTAAATTAAACCC
38331901 ATTACATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.52, C:0.32, G:0.05, T:0.11
Consensus pattern (22 bp):
CAAAGCAAACTAAATTAAACCC
Found at i:38337470 original size:28 final size:27
Alignment explanation
Indices: 38337426--38337489 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
38337416 CTGGACTTTG
* * *
38337426 GACATCATTAAAGCATGTAATAAAATTA
1 GACA-CATTAAAACATGCAATAAAATAA
*
38337454 GACACATTAATAACATGCATTAAAATAA
1 GACACATTAA-AACATGCAATAAAATAA
*
38337482 AACACATT
1 GACACATT
38337490 TATCACAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.27
Consensus pattern (27 bp):
GACACATTAAAACATGCAATAAAATAA
Found at i:38338668 original size:15 final size:15
Alignment explanation
Indices: 38338648--38338676 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38338638 CCATGTAGTG
38338648 GGATATGATTTATCA
1 GGATATGATTTATCA
38338663 GGATATGATTTATC
1 GGATATGATTTATC
38338677 TCTCTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (15 bp):
GGATATGATTTATCA
Found at i:38350722 original size:50 final size:50
Alignment explanation
Indices: 38350627--38350724 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
38350617 ACCAGACTGC
* *
38350627 ACAAGTAGAACCTATATAAAACTACTCTTCTTCTATTTTGTATTGATTGT
1 ACAAGTAGAACCTATATAAAACTACTCTCCTTCTATTTTGCATTGATTGT
* *
38350677 ACAAGTAGAATCC-GTATAAAACTTCTCTCCTTCTA-TTTGACATTGATT
1 ACAAGTAGAA-CCTATATAAAACTACTCTCCTTCTATTTTG-CATTGATT
38350725 AGAATAAGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 4 0.10
50 36 0.86
51 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (50 bp):
ACAAGTAGAACCTATATAAAACTACTCTCCTTCTATTTTGCATTGATTGT
Found at i:38368465 original size:24 final size:24
Alignment explanation
Indices: 38368437--38368485 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
38368427 ATAATTTGAA
*
38368437 ATTTAAAAGCATTGTATTTACACC
1 ATTTAAAAGCATCGTATTTACACC
*
38368461 ATTTAAAAGTATCGTATTTACACC
1 ATTTAAAAGCATCGTATTTACACC
38368485 A
1 A
38368486 ATTGTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (24 bp):
ATTTAAAAGCATCGTATTTACACC
Found at i:38377818 original size:131 final size:131
Alignment explanation
Indices: 38377574--38377840 Score: 498
Period size: 131 Copynumber: 2.0 Consensus size: 131
38377564 TTCATTTGCT
*
38377574 TTACAAAGAAAATTTCACACTGAACATTCTTTTATTCTTCTAATGGAACTTTGTAAAGAAACTCA
1 TTACCAAGAAAATTTCACACTGAACATTCTTTTATTCTTCTAATGGAACTTTGTAAAGAAACTCA
*
38377639 ATACATAAGTCCAGAAATAGATAATGTTCATCTGAGCTAATCAGAAATAGAAATATATGTGTCAG
66 ATACATAAGTCCAGAAATAGATAATGCTCATCTGAGCTAATCAGAAATAGAAATATATGTGTCAG
38377704 G
131 G
*
38377705 TTACCAAGACAATTTCACACTGAACATTCTTTTATTCTTCTAATGGAACTTTGTAAAGAAACTCA
1 TTACCAAGAAAATTTCACACTGAACATTCTTTTATTCTTCTAATGGAACTTTGTAAAGAAACTCA
*
38377770 ATACATAAGTCCAGAAATAGATAATGCTCATCTGAGCTAATCAGAAATAGAAATATATGTGTTAG
66 ATACATAAGTCCAGAAATAGATAATGCTCATCTGAGCTAATCAGAAATAGAAATATATGTGTCAG
38377835 G
131 G
38377836 TTACC
1 TTACC
38377841 CATCCGGGCT
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 132 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (131 bp):
TTACCAAGAAAATTTCACACTGAACATTCTTTTATTCTTCTAATGGAACTTTGTAAAGAAACTCA
ATACATAAGTCCAGAAATAGATAATGCTCATCTGAGCTAATCAGAAATAGAAATATATGTGTCAG
G
Found at i:38390215 original size:40 final size:40
Alignment explanation
Indices: 38390166--38390254 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
38390156 AGCGGCATTT
* *
38390166 TTAGTGGCGTTTGGACAAAAAACG-CGCTAAAAATTGAGCA
1 TTAGCGGCGTTT-GACAAAAAACGCCGCTAAAAATCGAGCA
* ** * *
38390206 TTAGCGGCGTTTTATGAAAAGCGCCGCTAAAGATCGAGCA
1 TTAGCGGCGTTTGACAAAAAACGCCGCTAAAAATCGAGCA
38390246 TTAGCGGCG
1 TTAGCGGCG
38390255 CTTTAAGGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 7 0.17
40 34 0.83
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGTTTGACAAAAAACGCCGCTAAAAATCGAGCA
Found at i:38390267 original size:40 final size:39
Alignment explanation
Indices: 38390190--38390292 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 39
38390180 ACAAAAAACG
* *
38390190 CGCTAAAAATTGAGCATTAGCGGCGTTTTATGAAAAGCGC
1 CGCTAAAAA-TGAGCATTAGCGGCGCTTTAAGAAAAGCGC
* * *
38390230 CGCTAAAGATCGAGCATTAGCGGCGCTTTAAGGAAAGCGT
1 CGCTAAAAAT-GAGCATTAGCGGCGCTTTAAGAAAAGCGC
* *
38390270 CACTAAAAATGAGTATTAGCGGC
1 CGCTAAAAATGAGCATTAGCGGC
38390293 ATTTTATGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 13 0.24
40 41 0.76
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.22
Consensus pattern (39 bp):
CGCTAAAAATGAGCATTAGCGGCGCTTTAAGAAAAGCGC
Found at i:38390427 original size:41 final size:39
Alignment explanation
Indices: 38390353--38390575 Score: 232
Period size: 41 Copynumber: 5.5 Consensus size: 39
38390343 AACCTTTCGG
** * *
38390353 GGCTTTAGCGGCGTTTTTGAAAAAGCACAGCTAATGCTCA
1 GGCTTTAGCGGCGTTTTTG-GGAAGCGCCGCTAATGCTCA
*
38390393 GGACATTAGCGGCGTTTTTGCGGAAGCGCCGCTAATGCTCAA
1 GG-CTTTAGCGGCGTTTTTG-GGAAGCGCCGCTAATGCTC-A
* ** *
38390435 GGCTTTAGCAGCAATTTTGGACAAGCGCCGCTAATG-TGCA
1 GGCTTTAGCGGCGTTTTTGG-GAAGCGCCGCTAATGCT-CA
* *
38390475 GGGCTTTAGCGGCGTTTTTGCGAATGCACCGCTAATGCTCA
1 -GGCTTTAGCGGCGTTTTTGGGAA-GCGCCGCTAATGCTCA
* *
38390516 GGGCTTTAGCGTCGTTTTTGGATAAGCGCCGCTAATGCTCA
1 -GGCTTTAGCGGCGTTTTTGG-GAAGCGCCGCTAATGCTCA
38390557 GGCTTTAGCGGCGTTTTTG
1 GGCTTTAGCGGCGTTTTTG
38390576 AAAAAGTGCC
Statistics
Matches: 153, Mismatches: 22, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
40 25 0.16
41 122 0.80
42 6 0.04
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (39 bp):
GGCTTTAGCGGCGTTTTTGGGAAGCGCCGCTAATGCTCA
Found at i:38390490 original size:82 final size:81
Alignment explanation
Indices: 38390382--38390575 Score: 268
Period size: 82 Copynumber: 2.4 Consensus size: 81
38390372 AAAAAGCACA
* *
38390382 GCTAATGCTCAGGACATTAGCGGCGTTTTTGCGGAA-GCGCCGCTAATGCTCAAGGCTTTAGCAG
1 GCTAATGCTCAGG-CTTTAGCGGCGTTTTTGC-GAATGCACCGCTAATGCTCAAGGCTTTAGC-G
38390446 -CAATTTTGGACAAGCGCC
63 TCAATTTTGGACAAGCGCC
*
38390464 GCTAATG-TGCAGGGCTTTAGCGGCGTTTTTGCGAATGCACCGCTAATGCTCAGGGCTTTAGCGT
1 GCTAATGCT-CA-GGCTTTAGCGGCGTTTTTGCGAATGCACCGCTAATGCTCAAGGCTTTAGCGT
** *
38390528 CGTTTTTGGATAAGCGCC
64 CAATTTTGGACAAGCGCC
38390546 GCTAATGCTCAGGCTTTAGCGGCGTTTTTG
1 GCTAATGCTCAGGCTTTAGCGGCGTTTTTG
38390576 AAAAAGTGCC
Statistics
Matches: 101, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
81 24 0.24
82 74 0.73
83 3 0.03
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (81 bp):
GCTAATGCTCAGGCTTTAGCGGCGTTTTTGCGAATGCACCGCTAATGCTCAAGGCTTTAGCGTCA
ATTTTGGACAAGCGCC
Found at i:38390935 original size:14 final size:14
Alignment explanation
Indices: 38390918--38390954 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
38390908 GGGTTTAATA
*
38390918 TATATTGTTTAGGG
1 TATATGGTTTAGGG
*
38390932 TATATGGTTTAGGT
1 TATATGGTTTAGGG
38390946 TATATGGTT
1 TATATGGTT
38390955 AATTTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:38392198 original size:23 final size:21
Alignment explanation
Indices: 38392156--38392198 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38392146 CCCTTCCCTC
*
38392156 CAAAACCCAAATTCCTTCAAG
1 CAAAACCCAAACTCCTTCAAG
38392177 CAAAACCCAAACCCTCCTTCAA
1 CAAAACCCAAA--CTCCTTCAA
38392199 ATTATCCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.16
Consensus pattern (21 bp):
CAAAACCCAAACTCCTTCAAG
Found at i:38393659 original size:14 final size:14
Alignment explanation
Indices: 38393640--38393669 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38393630 CATTTTACAC
38393640 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
38393654 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
38393668 AA
1 AA
38393670 CATGTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.27, G:0.20, T:0.07
Consensus pattern (14 bp):
AAACGCCGCTAAAG
Found at i:38393697 original size:57 final size:57
Alignment explanation
Indices: 38393600--38393710 Score: 188
Period size: 57 Copynumber: 1.9 Consensus size: 57
38393590 TTTTTAAAAG
*
38393600 CGCCACTAAAGAACATGTTCTTTAGCGGCGCATTTTACACAAACGCCGCTAAAGAAA
1 CGCCACTAAAGAACATGTTCTTTAGCGGCGCATTTAACACAAACGCCGCTAAAGAAA
*
38393657 CGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TTCTAACACAAACGCCGCTAAAG
1 CGCCACTAAAGAACATGTTCTTTAGCGGCGCATT-TAACACAAACGCCGCTAAAG
38393711 CTAATGTTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
56 2 0.04
57 49 0.96
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (57 bp):
CGCCACTAAAGAACATGTTCTTTAGCGGCGCATTTAACACAAACGCCGCTAAAGAAA
Found at i:38393718 original size:43 final size:43
Alignment explanation
Indices: 38393654--38393746 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 43
38393644 GCCGCTAAAG
38393654 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTCTAACAC
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTCTAACAC
* * *
38393697 AAACGCCGCTAAAGCTA-ATGTTCTTTAGCGGCGCTTTTTACAC
1 AAACGCCGCTAAAG-AACATGTTCTTTAGCGGCGCTTCTAACAC
38393740 AAACGCC
1 AAACGCC
38393747 ACTTTTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTCTAACAC
Found at i:38394184 original size:66 final size:66
Alignment explanation
Indices: 38394099--38394229 Score: 217
Period size: 66 Copynumber: 2.0 Consensus size: 66
38394089 CTGCAGCCTC
* * *
38394099 TGCTTCTCTGGATGCCGCATCAGCTTTAAGTTGTTGCTGGAGTTCTTCATATTTCTTTTGAACCT
1 TGCTTCTCTCGATGCCGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAACCT
38394164 A
66 A
* *
38394165 TGCTTCTCTCGCTGCCGCATCTGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAACCT
1 TGCTTCTCTCGATGCCGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAACCT
38394230 CAACTGNNNN
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (66 bp):
TGCTTCTCTCGATGCCGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAACCT
A
Found at i:38399482 original size:9 final size:9
Alignment explanation
Indices: 38399468--38399524 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
38399458 ATTATATATT
*
38399468 TAAATTTTG
1 TAAATTATG
38399477 TAAATTATG
1 TAAATTATG
38399486 --AATTATG
1 TAAATTATG
38399493 TAAATTATG
1 TAAATTATG
* *
38399502 TAAAATACG
1 TAAATTATG
*
38399511 TAAGTTATG
1 TAAATTATG
38399520 -AAATT
1 TAAATT
38399525 TGAACCTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 7 0.18
8 4 0.10
9 28 0.72
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (9 bp):
TAAATTATG
Found at i:38399494 original size:16 final size:16
Alignment explanation
Indices: 38399470--38399501 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38399460 TATATATTTA
*
38399470 AATTTTGTAAATTATG
1 AATTATGTAAATTATG
38399486 AATTATGTAAATTATG
1 AATTATGTAAATTATG
38399502 TAAAATACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
AATTATGTAAATTATG
Found at i:38399695 original size:29 final size:29
Alignment explanation
Indices: 38399654--38399711 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
38399644 CAAAATATAT
*
38399654 TTTTGGAAATGAAATAGTTGACAAATGGA
1 TTTTAGAAATGAAATAGTTGACAAATGGA
38399683 TTTTAGAAATGAAATAGTTGACAAATGGA
1 TTTTAGAAATGAAATAGTTGACAAATGGA
38399712 AGAAGATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (29 bp):
TTTTAGAAATGAAATAGTTGACAAATGGA
Found at i:38403643 original size:22 final size:21
Alignment explanation
Indices: 38403604--38403644 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
38403594 ACTCTGACTA
38403604 TAAAAACTAAACTCCAAACTT
1 TAAAAACTAAACTCCAAACTT
38403625 TAAAACACTAAA-TCACAAAC
1 TAAAA-ACTAAACTC-CAAAC
38403645 CCAATATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAAAACTAAACTCCAAACTT
Found at i:38403718 original size:14 final size:14
Alignment explanation
Indices: 38403701--38403782 Score: 51
Period size: 16 Copynumber: 5.4 Consensus size: 14
38403691 CATACCATAG
38403701 TAAACATTAAACCT
1 TAAACATTAAACCT
*
38403715 TAAACTATAAAACCCT
1 TAAAC-ATTAAA-CCT
38403731 TAAAC--TACATACCAT
1 TAAACATTA-A-ACC-T
38403746 AGTAAACATTAAACCT
1 --TAAACATTAAACCT
*
38403762 TAAACTATAAAACCCT
1 TAAAC-ATTAAA-CCT
38403778 TAAAC
1 TAAAC
38403783 TACATACTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
13 1 0.02
14 13 0.24
15 12 0.22
16 17 0.31
17 8 0.15
18 1 0.02
19 2 0.04
ACGTcount: A:0.50, C:0.23, G:0.01, T:0.26
Consensus pattern (14 bp):
TAAACATTAAACCT
Found at i:38403719 original size:47 final size:47
Alignment explanation
Indices: 38403661--38403794 Score: 250
Period size: 47 Copynumber: 2.9 Consensus size: 47
38403651 TAACAAACCC
*
38403661 TAAACCATAAACTATAAAACCCTTAAACTACATACCATAGTAAACAT
1 TAAACCTTAAACTATAAAACCCTTAAACTACATACCATAGTAAACAT
38403708 TAAACCTTAAACTATAAAACCCTTAAACTACATACCATAGTAAACAT
1 TAAACCTTAAACTATAAAACCCTTAAACTACATACCATAGTAAACAT
*
38403755 TAAACCTTAAACTATAAAACCCTTAAACTACATACTATAG
1 TAAACCTTAAACTATAAAACCCTTAAACTACATACCATAG
38403795 CCCTTAAACC
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 85 1.00
ACGTcount: A:0.49, C:0.23, G:0.02, T:0.25
Consensus pattern (47 bp):
TAAACCTTAAACTATAAAACCCTTAAACTACATACCATAGTAAACAT
Found at i:38404362 original size:40 final size:41
Alignment explanation
Indices: 38404220--38404377 Score: 232
Period size: 41 Copynumber: 3.9 Consensus size: 41
38404210 AGGCCTGCGA
* *
38404220 ATTAGCGGCGCAT-CAATAAAAACGCTGCTAAAGCCCAGAAC
1 ATTAGCGGCGCTTAC-ATAAAAACGCCGCTAAAGCCCAGAAC
* *
38404261 ATTAGCGGCGCTTA-ATTAAAAACGCCACTAAATCCCAGAAC
1 ATTAGCGGCGCTTACA-TAAAAACGCCGCTAAAGCCCAGAAC
*
38404302 ATTAGCGGCGCTTACATAAAAACGCCGCGAAAGCCCAGAAC
1 ATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAAC
38404343 ATTA-CGGCGCTTACATAAAAACGCCGCTAAAGCCC
1 ATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCC
38404378 CCGAAAAGTC
Statistics
Matches: 106, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
40 31 0.29
41 74 0.70
42 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.16
Consensus pattern (41 bp):
ATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAAC
Found at i:38406508 original size:192 final size:191
Alignment explanation
Indices: 38406250--38406607 Score: 472
Period size: 192 Copynumber: 1.9 Consensus size: 191
38406240 GTAATCTATA
* * * **
38406250 ATGGGTTTAAGTCATGGTTTTCATTTGGAGCTTTGTGATTAAAACACTATTATTACTTGAATGGA
1 ATGGGTTCAAGTCATGGTTTTCATTTGGAACTTTGTGATTAAAACACAACAATTACTTGAATGGA
* * * * * * * *
38406315 AATGCATTTGCATTTGT-GTATCCTACAATGCTT-TTTAATTGAACTTTGGGGTTGGAATTGTTA
66 AATGCACTTGCATTT-TCATATCCTACAAAGCTTCTTT-AGTCAACTTTGGAGTTGAAATTATTA
*
38406378 TTAGGAAGTAATTGATG-TTTTTATGTTGATGTTAATGAATACAGTAGACTAAGTTGAATTTTTT
129 TTAGGAAGTAATTGATGATTTTT-T-ATGATGTTAATGAATACAGTAGACTAAGTTGAATTTTTT
*
38406442 ATGGGTTCAAGTCATGGTTTTCATTT-GAACTTTGTGATTACAACACAACAATTTACTTGAATGG
1 ATGGGTTCAAGTCATGGTTTTCATTTGGAACTTTGTGATTAAAACACAACAA-TTACTTGAATGG
** *
38406506 AAATGCACTTGTGTTTTCATATCCTGCAAAGCTTCTTTAGTCAACTTTGGAGTTGAAATTATTAT
65 AAATGCACTTGCATTTTCATATCCTACAAAGCTTCTTTAGTCAACTTTGGAGTTGAAATTATTAT
*
38406571 TAGGATGTAATTGATGATTTTTTATGATGTTAATGAA
130 TAGGAAGTAATTGATGATTTTTTATGATGTTAATGAA
38406608 CATAATAGAC
Statistics
Matches: 143, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
191 34 0.24
192 101 0.71
193 8 0.06
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (191 bp):
ATGGGTTCAAGTCATGGTTTTCATTTGGAACTTTGTGATTAAAACACAACAATTACTTGAATGGA
AATGCACTTGCATTTTCATATCCTACAAAGCTTCTTTAGTCAACTTTGGAGTTGAAATTATTATT
AGGAAGTAATTGATGATTTTTTATGATGTTAATGAATACAGTAGACTAAGTTGAATTTTTT
Found at i:38407672 original size:43 final size:43
Alignment explanation
Indices: 38407611--38407891 Score: 282
Period size: 43 Copynumber: 6.6 Consensus size: 43
38407601 ATATTTAATA
*
38407611 CTAAAGGTCTTG-GTCTATAGCGGCGTTTGTGGAGAAAGCGCCA
1 CTAAAGGTCTTGAG-CTATAGCGGCGTTTGTGGAGAAAGCGCCG
* **
38407654 CTAAAGGTCTTGAGCTATAGTGGCGTTTGTGG-GAAAAGTACCG
1 CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAG-AAAGCGCCG
* *
38407697 CTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGAGAAAGCGACG
1 CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAGAAAGCGCCG
* ** * * * *
38407740 CTAAAGATCTCAAGCTATAGCGGCGATTGTGTA-AAAACGTCG
1 CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAGAAAGCGCCG
** * *
38407782 CTAAAGGTCTTGATTTTTAGCGGCGTTTGTGGAAAAAGCGCCG
1 CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAGAAAGCGCCG
* * * *
38407825 CTAAAGGTCCTGACCTATAGCGGCGTTTGTAGGA-AAAACGTCG
1 CTAAAGGTCTTGAGCTATAGCGGCGTTTGT-GGAGAAAGCGCCG
* * **
38407868 CTAAATGTCATGATTTATAGCGGC
1 CTAAAGGTCTTGAGCTATAGCGGC
38407892 ATTTATTTCT
Statistics
Matches: 196, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
42 33 0.17
43 158 0.81
44 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (43 bp):
CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAGAAAGCGCCG
Found at i:38407891 original size:128 final size:129
Alignment explanation
Indices: 38407625--38407872 Score: 338
Period size: 128 Copynumber: 1.9 Consensus size: 129
38407615 AGGTCTTGGT
* * * *
38407625 CTATAGCGGCGTTTGTGGAGAAAGCGCCACTAAAGGTCTTGAGCTATAGTGGCGTTTGTGGGAAA
1 CTATAGCGGCGATTGTGGAGAAAACGCCACTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAAA
* * *
38407690 AGTACCGCTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGAGAAAGCGACGCTAAAGATCTCAAG
66 AGCACCGCTAAAGGTCCTGACCTATAGCGGCGTTTGTGGAGAAAACGACGCTAAAGATCTCAAG
* * * ** *
38407754 CTATAGCGGCGATTGTGTA-AAAACGTCGCTAAAGGTCTTGATTTTTAGCGGCGTTTGTGGAAAA
1 CTATAGCGGCGATTGTGGAGAAAACGCCACTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAAA
* *
38407818 AGCGCCGCTAAAGGTCCTGACCTATAGCGGCGTTTGTAGGA-AAAACGTCGCTAAA
66 AGCACCGCTAAAGGTCCTGACCTATAGCGGCGTTTGT-GGAGAAAACGACGCTAAA
38407873 TGTCATGATT
Statistics
Matches: 103, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
128 83 0.81
129 20 0.19
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (129 bp):
CTATAGCGGCGATTGTGGAGAAAACGCCACTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAAA
AGCACCGCTAAAGGTCCTGACCTATAGCGGCGTTTGTGGAGAAAACGACGCTAAAGATCTCAAG
Found at i:38413928 original size:70 final size:70
Alignment explanation
Indices: 38413810--38415509 Score: 1439
Period size: 70 Copynumber: 24.3 Consensus size: 70
38413800 TATGATCCCT
* ** * * * *
38413810 TCCAAAACAGTTAGCGCAAGCTCAAGCTCCCAGCTAAAAACTTTAGGCTCACAGGTCCAATACCA
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
***
38413875 CAATA
66 CAGCC
* * * * * **
38413880 TCCAAAACAGTTAGCATGAGCTCAAGCTCCCAACTATAATCTTAAGGCTCACAAGTTCAATATTG
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
*
38413945 CAACC
66 CAGCC
* * * ** **
38413950 TCCAAAATAGTTAGAGTGAGCTCAAGCTCCAAGTTGAAAA-CTTAAGGCTCGTAGGTTCAATATT
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCT-AAAATCTTAAGGCTCACAGGTTCAATACC
*
38414014 GTAGCC
65 GCAGCC
* * *
38414020 TCCAAAATAGTTAGTGTGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCACAGGTTCAATATCG
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
*
38414085 CAACC
66 CAGCC
* * * ***
38414090 T-CAAAAAAGTTAGCAAG-GA-TTCAAGCTCCCAGCTAAAATCTTAAAGCTTGTAGGTTCAATAC
1 TCCAAAATAGTTAGC--GTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATAC
*
38414152 TGCAGCC
64 CGCAGCC
* * ** * *
38414159 TCTAAAATAGTTAGTGCAAGCTCAAGCTCCCAAG-TAAAATTTTAAGGCTTGA-AGGTTCAATAC
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCC-AGCTAAAATCTTAAGGC-TCACAGGTTCAATAC
38414222 CGCAGCC
64 CGCAGCC
* * *
38414229 TCCAAAATAGTTAGCATGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGA-AGGTTCAATACT
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTC-ACAGGTTCAATACC
*
38414293 GTAGCC
65 GCAGCC
* * * * * *
38414299 TCCAAACTAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAA-CATAAGGCTTGA-AGGTTCAACAT
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCT-AAAATCTTAAGGC-TCACAGGTTCAATAC
***
38414362 TATAGCC
64 CGCAGCC
* * * * **
38414369 TCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCTATAATTTTAAGGCTCGCATATTCAATACCG
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
38414434 CAGCC
66 CAGCC
* * *** * *
38414439 TCCAAAATAGTTAGCGAGAACTCAAGCTTTTAGCTAAAATCTTAAAGG-TCACAGGTTTAATATC
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTT-AAGGCTCACAGGTTCAATACC
*
38414503 ACAGCC
65 GCAGCC
* * *
38414509 TCTAAAATAGTTAGCGTGAGCTCAAGCTCCCAAG-TAAAATTTTAAGGCTTGA-AGGTTCAATAC
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCC-AGCTAAAATCTTAAGGC-TCACAGGTTCAATAC
38414572 CGCAGCC
64 CGCAGCC
* * * * *
38414579 TCTAAAATAGTTAGTGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCTA-AGGTTCAATACT
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTC-ACAGGTTCAATACC
*
38414643 GTAGCC
65 GCAGCC
* * * * *
38414649 TCCAAAATAATTAGCGTGAGCTCAAGCTCCAAGCTGAAAA-CTTAAGGCTTGA-AGGTTCAACAT
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCT-AAAATCTTAAGGC-TCACAGGTTCAATAC
***
38414712 TATAGCC
64 CGCAGCC
* * * *
38414719 TCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCTATAATCTTAAGGCTCGCATGTTCAATACCG
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
*
38414784 TAGCC
66 CAGCC
* * *** * * ** * * *
38414789 TCCAAAATAGTTAGCGAGAACTCAAGCTTTTAGTTAAAATCTTAAAGCTCACATATTTAATATCA
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
*
38414854 TAGCC
66 CAGCC
* * * * * *
38414859 TCTAAAATAGTTAGCGCGAGCTCAAGCTCCCAAG-TAAAATTTTAAGGCTTGA-AGGCTCAATGC
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCC-AGCTAAAATCTTAAGGC-TCACAGGTTCAATAC
38414922 CGCAGCC
64 CGCAGCC
* * * *
38414929 TCCAAAATAGTTAGCGCGAGTTCAAGCTCCCAGCTACAATCTTAAGGCTCGA-AGGTTCAATACT
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTC-ACAGGTTCAATACC
*
38414993 GTAGCC
65 GCAGCC
* * * *
38414999 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAA-CTTAAGGCTTGA-AGGTTCAACAT
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCT-AAAATCTTAAGGC-TCACAGGTTCAATAC
***
38415062 TATAGCC
64 CGCAGCC
* * ** * *
38415069 TCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAACTATGATCTTAAGGCTCGCATGTTCAATACCG
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
38415134 CAGCC
66 CAGCC
* ** * ** * *
38415139 TCTAAAATAGTTAGCAAGAACTCAAGCTTTCAGCTAAAATCTTAAAGG-TCACAGGTTTAATATC
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTT-AAGGCTCACAGGTTCAATACC
*
38415203 ACAGCC
65 GCAGCC
* * * * * *
38415209 TCTAAAATAGTTAGCGCGAGCTCAAGCTACCAGCTAAAATCTTAAGGCTCACAGGTTTAGTACCA
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
*
38415274 CATCC
66 CAGCC
* * * * * * * * *
38415279 TCCAAAACAGTTAGCGCGAGCTCAAGGTCCCAACTTAAATATTAAGGCTTACAAGTTTAATACC-
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
* *
38415343 AAACC
66 CAGCC
* * * * * * ** ** * *
38415348 TCTAAAACAGTCATCGAGGGCTCAAGCTCCCAGCTGTAATCTTAAGGCTTGCAAGTTTAATACCG
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
*
38415413 CAACC
66 CAGCC
* * * * * * * *
38415418 TCCAAAATAGTTAGCGCGAGCTTAAACTCCTAGTTGAAATCTTAAGG-TCCGCAAGTTCAATACC
1 TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCT-CACAGGTTCAATACC
*
38415482 GCTGCC
65 GCAGCC
*
38415488 TCCAAAATAGTTAACGTGAGCT
1 TCCAAAATAGTTAGCGTGAGCT
38415510 AAAACACCCA
Statistics
Matches: 1325, Mismatches: 268, Indels: 74
0.79 0.16 0.04
Matches are distributed among these distances:
68 1 0.00
69 142 0.11
70 1147 0.87
71 35 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (70 bp):
TCCAAAATAGTTAGCGTGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCACAGGTTCAATACCG
CAGCC
Found at i:38414609 original size:350 final size:350
Alignment explanation
Indices: 38413813--38415500 Score: 2166
Period size: 350 Copynumber: 4.8 Consensus size: 350
38413803 GATCCCTTCC
* * * * * *
38413813 AAAACAGTTAGCGCAAGCTCAAGCTCCC-AGCTAAAAACTTT-AGGC-TCACAGGTCCAATACCA
1 AAAATAGTTAGCGCGAGCTCAAGCTCCCAAG-T-AAAATTTTAAGGCTTGA-AGGTTCAATACCG
*** * ** * * *
38413875 CAATATCCAAAACAGTTAGCATGAGCTCAAGCTCCCAACTATAATCTTAAGGCTC-ACAAGTTCA
63 CAGCCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGA-AGGTTCA
* * * * * * *
38413939 ATATTGCAACCTCCAAAATAGTTAGAGTGAGCTCAAGCTCCAAGTTGAAAACTTAAGGCTCGTAG
127 ATACTGTAGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAACTTAAGGCTTGAAG
* * * * *
38414004 GTTCAATATTGTAGCCTCCAAAATAGTTAGTGTGAGCTCAAGCTCCCAGCTACAATCTTAAGGCT
192 GTTCAACATTATAGCCTCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCTATAATCTTAAGGCT
* * * * * * * **
38414069 CACAGGTTCAATATCGCAACCT-CAAAAAAGTTAGCAAGGATTCAAGCTCCCAGCTAAAATCTTA
257 CGCATGTTCAATACCGCAGCCTCCAAAATAGTTAGCAAGAACTCAAGCTTTCAGCTAAAATCTTA
*** * *
38414133 AAGCTTGTAGGTTCAATA-CTGCAGCCTCT
322 AAGCTCACAGGTTTAATATC-ACAGCCTCT
* *
38414162 AAAATAGTTAGTGCAAGCTCAAGCTCCCAAGTAAAATTTTAAGGCTTGAAGGTTCAATACCGCAG
1 AAAATAGTTAGCGCGAGCTCAAGCTCCCAAGTAAAATTTTAAGGCTTGAAGGTTCAATACCGCAG
**
38414227 CCTCCAAAATAGTTAGCATGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGAAGGTTCAATAC
66 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGAAGGTTCAATAC
* *
38414292 TGTAGCCTCCAAACTAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAACATAAGGCTTGAAGGTTC
131 TGTAGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAACTTAAGGCTTGAAGGTTC
*
38414357 AACATTATAGCCTCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCTATAATTTTAAGGCTCGCA
196 AACATTATAGCCTCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCTATAATCTTAAGGCTCGCA
* * * *
38414422 TATTCAATACCGCAGCCTCCAAAATAGTTAGCGAGAACTCAAGCTTTTAGCTAAAATCTTAAAGG
261 TGTTCAATACCGCAGCCTCCAAAATAGTTAGCAAGAACTCAAGCTTTCAGCTAAAATCTTAAAGC
38414487 TCACAGGTTTAATATCACAGCCTCT
326 TCACAGGTTTAATATCACAGCCTCT
*
38414512 AAAATAGTTAGCGTGAGCTCAAGCTCCCAAGTAAAATTTTAAGGCTTGAAGGTTCAATACCGCAG
1 AAAATAGTTAGCGCGAGCTCAAGCTCCCAAGTAAAATTTTAAGGCTTGAAGGTTCAATACCGCAG
* * *
38414577 CCTCTAAAATAGTTAGTGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCTAAGGTTCAATAC
66 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGAAGGTTCAATAC
*
38414642 TGTAGCCTCCAAAATAATTAGCGTGAGCTCAAGCTCCAAGCTGAAAACTTAAGGCTTGAAGGTTC
131 TGTAGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAACTTAAGGCTTGAAGGTTC
38414707 AACATTATAGCCTCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCTATAATCTTAAGGCTCGCA
196 AACATTATAGCCTCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCTATAATCTTAAGGCTCGCA
* * * *
38414772 TGTTCAATACCGTAGCCTCCAAAATAGTTAGCGAGAACTCAAGCTTTTAGTTAAAATCTTAAAGC
261 TGTTCAATACCGCAGCCTCCAAAATAGTTAGCAAGAACTCAAGCTTTCAGCTAAAATCTTAAAGC
** *
38414837 TCACATATTTAATATCATAGCCTCT
326 TCACAGGTTTAATATCACAGCCTCT
* *
38414862 AAAATAGTTAGCGCGAGCTCAAGCTCCCAAGTAAAATTTTAAGGCTTGAAGGCTCAATGCCGCAG
1 AAAATAGTTAGCGCGAGCTCAAGCTCCCAAGTAAAATTTTAAGGCTTGAAGGTTCAATACCGCAG
*
38414927 CCTCCAAAATAGTTAGCGCGAGTTCAAGCTCCCAGCTACAATCTTAAGGCTCGAAGGTTCAATAC
66 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGAAGGTTCAATAC
38414992 TGTAGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAACTTAAGGCTTGAAGGTTC
131 TGTAGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAACTTAAGGCTTGAAGGTTC
* *
38415057 AACATTATAGCCTCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAACTATGATCTTAAGGCTCGCA
196 AACATTATAGCCTCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCTATAATCTTAAGGCTCGCA
* *
38415122 TGTTCAATACCGCAGCCTCTAAAATAGTTAGCAAGAACTCAAGCTTTCAGCTAAAATCTTAAAGG
261 TGTTCAATACCGCAGCCTCCAAAATAGTTAGCAAGAACTCAAGCTTTCAGCTAAAATCTTAAAGC
38415187 TCACAGGTTTAATATCACAGCCTCT
326 TCACAGGTTTAATATCACAGCCTCT
* * * * * *
38415212 AAAATAGTTAGCGCGAGCTCAAGCTACC-AGCTAAAATCTTAAGGC-TCACAGGTTTAGTACCAC
1 AAAATAGTTAGCGCGAGCTCAAGCTCCCAAG-TAAAATTTTAAGGCTTGA-AGGTTCAATACCGC
* * * * * *
38415275 ATCCTCCAAAACAGTTAGCGCGAGCTCAAGGTCCCAACTTA-AATATTAAGGCTTAC-AA-GTTT
64 AGCCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGC-TACAATCTTAAGGC-T-CGAAGGTTC
** * * * * * * * * * *
38415337 AATAC-CAAACCTCTAAAACAGTCATCGAGGGCTCAAGCTCCCAGCTGTAATCTTAAGGCTTGCA
126 AATACTGTAGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAACTTAAGGCTTG-A
* * *** * * * * * *
38415401 AGTTTAATACCGCA-A-CCTCCAAAATAGTTAGCGCGAGCTTAAACTCCTAGTTGA-AATCTTAA
190 AGGTTCA-ACATTATAGCCTCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCT-ATAATCTTAA
* *
38415463 GG-TCCGCAAGTTCAATACCGCTGCCTCCAAAATAGTTA
253 GGCT-CGCATGTTCAATACCGCAGCCTCCAAAATAGTTA
38415501 ACGTGAGCTA
Statistics
Matches: 1197, Mismatches: 127, Indels: 30
0.88 0.09 0.02
Matches are distributed among these distances:
348 8 0.01
349 348 0.29
350 831 0.69
351 9 0.01
352 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (350 bp):
AAAATAGTTAGCGCGAGCTCAAGCTCCCAAGTAAAATTTTAAGGCTTGAAGGTTCAATACCGCAG
CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGAAGGTTCAATAC
TGTAGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAACTTAAGGCTTGAAGGTTC
AACATTATAGCCTCCAAAAGAGTTAGCGTGAGCTCAAGCTCCCAGCTATAATCTTAAGGCTCGCA
TGTTCAATACCGCAGCCTCCAAAATAGTTAGCAAGAACTCAAGCTTTCAGCTAAAATCTTAAAGC
TCACAGGTTTAATATCACAGCCTCT
Found at i:38415692 original size:18 final size:17
Alignment explanation
Indices: 38415671--38415725 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
38415661 CAATGCAAGC
38415671 TTGAAATTTTGCTTAAGT
1 TTGAAATTTT-CTTAAGT
*
38415689 TTG-AATGTTTACTTGAGT
1 TTGAAAT-TTT-CTTAAGT
38415707 TTGAAAATTTTCTTAAGT
1 TTG-AAATTTTCTTAAGT
38415725 T
1 T
38415726 CTTAAAGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 3 0.10
18 22 0.71
19 3 0.10
20 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (17 bp):
TTGAAATTTTCTTAAGT
Found at i:38420642 original size:154 final size:154
Alignment explanation
Indices: 38420357--38420672 Score: 578
Period size: 154 Copynumber: 2.0 Consensus size: 154
38420347 ATGCATATAT
* *
38420357 ATATGTGGCCTTACCATATTTGATGTGTGTTTAATATGATAGAATTATGAAAAGTAAAATGAGGT
1 ATAT-TGGCCTTACCATATTTGATGTGTGTTTAATAGGATAGAATGATGAAAAGTAAAATGAGGT
38420422 TTGAATATACATATATGTATTTGGTCATTTAGGTAAGTTTGGATACTTGGTTGACAAGTTTTTAA
65 TTGAATATACATATATGTATTTGGTCATTTAGGTAAGTTTGGATACTTGGTTGACAAGTTTTTAA
* *
38420487 GTTGTCATTTGAGGTGTCTAAGGGA
130 GTTGCCATTTGAGGTGTCTAAAGGA
38420512 ATATTGGCCTTACCATATTTGATGTGTGTTTAATAGGATAGAATGATGAAAAGTAAAATGAGGTT
1 ATATTGGCCTTACCATATTTGATGTGTGTTTAATAGGATAGAATGATGAAAAGTAAAATGAGGTT
38420577 TGAATATACATATATGTATTTGGTCATTTAGGTAAGTTTGGATACTTGGTTGACAAGTTTTTAAG
66 TGAATATACATATATGTATTTGGTCATTTAGGTAAGTTTGGATACTTGGTTGACAAGTTTTTAAG
*
38420642 TTGCCATTTGAGGTGTCTAAAGGC
131 TTGCCATTTGAGGTGTCTAAAGGA
38420666 ATATTGG
1 ATATTGG
38420673 TTGTATGTTG
Statistics
Matches: 156, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
154 152 0.97
155 4 0.03
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.39
Consensus pattern (154 bp):
ATATTGGCCTTACCATATTTGATGTGTGTTTAATAGGATAGAATGATGAAAAGTAAAATGAGGTT
TGAATATACATATATGTATTTGGTCATTTAGGTAAGTTTGGATACTTGGTTGACAAGTTTTTAAG
TTGCCATTTGAGGTGTCTAAAGGA
Found at i:38430414 original size:16 final size:16
Alignment explanation
Indices: 38430393--38430460 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
38430383 TTTGGTTCGC
38430393 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
38430409 TGTATTGGATTGGAGG
1 TGTATTGGATTAGAGG
38430425 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
38430441 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
38430457 TGTA
1 TGTA
38430461 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:38430717 original size:18 final size:17
Alignment explanation
Indices: 38430696--38430730 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38430686 TTATTATTAA
*
38430696 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38430714 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38430731 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:38430784 original size:157 final size:157
Alignment explanation
Indices: 38430583--38431056 Score: 876
Period size: 157 Copynumber: 3.0 Consensus size: 157
38430573 TAGAATACCC
* * *
38430583 TTAGCATAAATTTGTTTTAGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
38430648 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
38430713 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
38430740 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
38430805 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
38430870 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
38430897 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
38430962 ATATCAATAATAAATAATTTAATCATATTTTAAACATAATTTATTATTAAATATATTATAATTAA
66 ATATCAATAATAAATAATTTAATCATA-TTTAAACATAA-TTATTATTAAATATATTATAATTAA
38431027 AATATATAATTTAATAAAATTCTTAATAA
129 AATATATAATTTAATAAAATTCTTAATAA
38431056 T
1 T
38431057 CAATATTCTT
Statistics
Matches: 309, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
157 243 0.79
158 11 0.04
159 55 0.18
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:38430870 original size:16 final size:16
Alignment explanation
Indices: 38430833--38430874 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38430823 TTAATCATAT
*
38430833 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
38430849 TT-AAATATATTATAA
1 TTAAAATATATTATAA
38430864 TTAAAATATAT
1 TTAAAATATAT
38430875 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:38430881 original size:14 final size:15
Alignment explanation
Indices: 38430842--38430883 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38430832 TTTAAACATA
*
38430842 ATTATTATTAAATAT
1 ATTATAATTAAATAT
38430857 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
38430871 A-TATAATTTAATA
1 ATTATAATTAAATA
38430884 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:38431040 original size:14 final size:15
Alignment explanation
Indices: 38431002--38431042 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
38430992 TAAACATAAT
*
38431002 TTATTATTAAATATA
1 TTATAATTAAATATA
38431017 TTATAATTAAA-ATA
1 TTATAATTAAATATA
*
38431031 -TATAATTTAATA
1 TTATAATTAAATA
38431043 AAATTCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATAATTAAATATA
Done.