Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 19
Found at i:534 original size:31 final size:30
Alignment explanation
Indices: 478--535 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
468 GTGACCAAAA
*
478 TAAAATTTGAAAAGTTTGGTGACCAAAGTG
1 TAAAATTTGAAAAGTTTGGTAACCAAAGTG
*
508 TAAACTTTGGAAAAGTTTAGG-AACCAAA
1 TAAAATTT-GAAAAGTTT-GGTAACCAAA
536 ATGGTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.29
31 15 0.62
32 2 0.08
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (30 bp):
TAAAATTTGAAAAGTTTGGTAACCAAAGTG
Found at i:956 original size:30 final size:31
Alignment explanation
Indices: 899--960 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
889 TATTCACTTA
899 TGGAAGATGATAAGGTTTAGGTATCTTGGTT
1 TGGAAGATGATAAGGTTTAGGTATCTTGGTT
*
930 TGGAAGATGATAAGG-TTAGGTGTCTTGGTT
1 TGGAAGATGATAAGGTTTAGGTATCTTGGTT
960 T
1 T
961 AATGGTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.24, C:0.03, G:0.34, T:0.39
Consensus pattern (31 bp):
TGGAAGATGATAAGGTTTAGGTATCTTGGTT
Found at i:2597 original size:38 final size:39
Alignment explanation
Indices: 2541--2641 Score: 127
Period size: 38 Copynumber: 2.6 Consensus size: 39
2531 ACTAAGTGTA
2541 ATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTG
1 ATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTG
* * * *
2580 -TATGGTGGGAACAACCTTA--TGTAATGCACTTTGGTG
1 ATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTG
*
2616 TATATGGTGGGCATGACCTTATGTGT
1 -ATATGGTGGGCACGACCTTATGTGT
2642 GCACTACGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
36 15 0.29
38 33 0.65
40 3 0.06
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.34
Consensus pattern (39 bp):
ATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTG
Found at i:2610 original size:36 final size:37
Alignment explanation
Indices: 2542--2618 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
2532 CTAAGTGTAA
* *
2542 TATGGTGGGCACGACCTTATGTGTAATACACTTCGGTG
1 TATGGTGGGAACAACCTTA-GTGTAATACACTTCGGTG
* *
2580 TATGGTGGGAACAACCTTA-TGTAATGCACTTTGGTG
1 TATGGTGGGAACAACCTTAGTGTAATACACTTCGGTG
2616 TAT
1 TAT
2619 ATGGTGGGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 18 0.51
38 17 0.49
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (37 bp):
TATGGTGGGAACAACCTTAGTGTAATACACTTCGGTG
Found at i:3987 original size:21 final size:19
Alignment explanation
Indices: 3937--4016 Score: 60
Period size: 18 Copynumber: 4.3 Consensus size: 19
3927 TTTATTTTAA
*
3937 TAATATATAATAA-ATTAT
1 TAATATTTAATAATATTAT
* *
3955 TAATAATGAATAATATTATT
1 TAATATTTAATAATATTA-T
3975 TATATATTTAATAATA-TAT
1 TA-ATATTTAATAATATTAT
* *
3994 T-ATAATCTAAAAATATT-T
1 TAAT-ATTTAATAATATTAT
4012 TAATA
1 TAATA
4017 AAGATAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
17 2 0.04
18 22 0.45
19 9 0.18
20 5 0.10
21 11 0.22
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
TAATATTTAATAATATTAT
Found at i:3993 original size:12 final size:13
Alignment explanation
Indices: 3895--3999 Score: 58
Period size: 13 Copynumber: 7.8 Consensus size: 13
3885 AATAATCAAT
3895 TATATTATAATAA
1 TATATTATAATAA
*
3908 TATAATATAGATATTA
1 TATATTATA-ATA--A
* **
3924 TATTTTATTTTAA
1 TATATTATAATAA
3937 TA-ATATATAATAA
1 TATAT-TATAATAA
3950 -ATTATTAATAATGAA
1 TA-TATT-ATAAT-AA
*
3965 TAATATTAT--TTA
1 T-ATATTATAATAA
3977 TATATT-TAATAA
1 TATATTATAATAA
3989 TATATTATAAT
1 TATATTATAAT
4000 CTAAAAATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 26
0.66 0.10 0.25
Matches are distributed among these distances:
10 1 0.01
11 5 0.07
12 12 0.17
13 23 0.33
14 10 0.14
15 6 0.09
16 11 0.16
17 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
TATATTATAATAA
Found at i:4167 original size:18 final size:19
Alignment explanation
Indices: 4135--4170 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4125 TATTTTATTA
*
4135 ATAATATAATTAATATTTT
1 ATAATATAATAAATATTTT
4154 ATAATA-AATAAATATTT
1 ATAATATAATAAATATTT
4171 AATATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATATAATAAATATTTT
Found at i:4214 original size:44 final size:47
Alignment explanation
Indices: 4117--4224 Score: 107
Period size: 44 Copynumber: 2.4 Consensus size: 47
4107 AAAATATACC
* *
4117 AATATTTTTAT-TTTATTAATAATATAATTAATATTTTATAATAAATA
1 AATATTTATATATTTA-AAATAATATAATTAATATTTTATAATAAATA
* * *
4164 AATATTTA-ATATTTAAAATAATAT-ATTAA-GTTTTATGATAGATA
1 AATATTTATATATTTAAAATAATATAATTAATATTTTATAATAAATA
** *
4208 TTTATTTATGTATTTAA
1 AATATTTATATATTTAA
4225 TATTTGTAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
44 18 0.35
45 12 0.24
46 10 0.20
47 11 0.22
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (47 bp):
AATATTTATATATTTAAAATAATATAATTAATATTTTATAATAAATA
Found at i:18473 original size:23 final size:22
Alignment explanation
Indices: 18439--18482 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18429 ATTATTTTCT
*
18439 AACTTATAATGAAGTATAAAATA
1 AACTTATAATG-AGAATAAAATA
18462 AACTTGAT-ATGAGAATAAAAT
1 AACTT-ATAATGAGAATAAAAT
18483 GGCATAGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 8 0.42
24 2 0.11
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (22 bp):
AACTTATAATGAGAATAAAATA
Found at i:23175 original size:25 final size:28
Alignment explanation
Indices: 23110--23178 Score: 72
Period size: 31 Copynumber: 2.5 Consensus size: 28
23100 GTTCTAACGC
*
23110 AATAAAAATTAAATATATTTGGTTGTGA
1 AATAAAAATTAAATATAATTGGTTGTGA
*
23138 AATTATACCAATTAAATATAATTGG-T-T-A
1 AA-TA-A-AAATTAAATATAATTGGTTGTGA
23166 AATAAAAATTAAA
1 AATAAAAATTAAA
23179 AAATATTGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
25 7 0.20
26 1 0.03
27 2 0.06
28 5 0.14
29 3 0.09
30 2 0.06
31 15 0.43
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (28 bp):
AATAAAAATTAAATATAATTGGTTGTGA
Found at i:27180 original size:16 final size:16
Alignment explanation
Indices: 27159--27190 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27149 CTAAAAATTA
27159 TGATTTACTGATTTAT
1 TGATTTACTGATTTAT
*
27175 TGATTTACTGGTTTAT
1 TGATTTACTGATTTAT
27191 GAACCATGGC
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:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (16 bp):
TGATTTACTGATTTAT
Found at i:29205 original size:17 final size:16
Alignment explanation
Indices: 29183--29231 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
29173 AAATTAGAGC
29183 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAG-AAAG
*
29200 ACAAAAAG-AAGAAAT
1 ACAAAAAGAAAGAAAG
*
29215 TCAAAAAGAAAGCAAAG
1 ACAAAAAGAAAG-AAAG
29232 CCAAGGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 10 0.37
16 6 0.22
17 11 0.41
ACGTcount: A:0.71, C:0.08, G:0.16, T:0.04
Consensus pattern (16 bp):
ACAAAAAGAAAGAAAG
Found at i:29464 original size:17 final size:17
Alignment explanation
Indices: 29421--29465 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
29411 CCTTAAATCC
**
29421 TTTCTTCTACCTTTCCA
1 TTTCTTCTATTTTTCCA
29438 TTTCTTCTATTTTTCCA
1 TTTCTTCTATTTTTCCA
29455 TTTCTTCTATT
1 TTTCTTCTATT
29466 CCTTTCTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTCTTCTATTTTTCCA
Found at i:33638 original size:2 final size:2
Alignment explanation
Indices: 33625--33666 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
33615 TTATTTTCAA
* *
33625 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33666 A
1 A
33667 GTTATTATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39858 original size:21 final size:21
Alignment explanation
Indices: 39832--39887 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
39822 TTTTAATGTT
39832 TTAAGCTTATATAAGCTGTCC
1 TTAAGCTTATATAAGCTGTCC
*
39853 TTAAGCTTATATAAGCTTTCC
1 TTAAGCTTATATAAGCTGTCC
39874 TTAAGCTTATATAA
1 TTAAGCTTATATAA
39888 CACTCAAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (21 bp):
TTAAGCTTATATAAGCTGTCC
Found at i:44294 original size:20 final size:20
Alignment explanation
Indices: 44254--44292 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
44244 CATTGCAGGA
*
44254 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
44274 ATTTAATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
44293 GACTTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:44526 original size:65 final size:65
Alignment explanation
Indices: 44444--44574 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
44434 TCTCATCCAC
44444 AAGGTAGTCTCCCTAGTGATACTGAGGTCACTAAACATCATGGAAAGGAGCAGCATAGTGTACTT
1 AAGGTAGTCTCCCTAGTGATACTGAGGTCACTAAACATCATGGAAAGGAGCAGCATAGTGTACTT
* *
44509 AAGGTATTCTCCCTAGTGATATTGAGGTCACTAAACATCATGGAAAGGAGCAGCATAGTGTACTT
1 AAGGTAGTCTCCCTAGTGATACTGAGGTCACTAAACATCATGGAAAGGAGCAGCATAGTGTACTT
44574 A
1 A
44575 CACTAAGGAG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (65 bp):
AAGGTAGTCTCCCTAGTGATACTGAGGTCACTAAACATCATGGAAAGGAGCAGCATAGTGTACTT
Found at i:45623 original size:18 final size:18
Alignment explanation
Indices: 45600--45637 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
45590 ACAAAACCTA
45600 AAGATTTGTAATAAGCTC
1 AAGATTTGTAATAAGCTC
45618 AAGATTTGTAATAAGCTC
1 AAGATTTGTAATAAGCTC
45636 AA
1 AA
45638 AACACACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (18 bp):
AAGATTTGTAATAAGCTC
Found at i:45713 original size:26 final size:26
Alignment explanation
Indices: 45661--45739 Score: 140
Period size: 26 Copynumber: 3.0 Consensus size: 26
45651 TTACAAGAGA
45661 AAGGAAAATAAGAATAAAAAAGCTCTT
1 AAGGAAAATAAGAAT-AAAAAGCTCTT
45688 AAGGAAAATAAGAATAAAAAGCTCTT
1 AAGGAAAATAAGAATAAAAAGCTCTT
*
45714 AAGGAAAATAAGAATAGAAAGCTCTT
1 AAGGAAAATAAGAATAAAAAGCTCTT
45740 CTCTTGTGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 36 0.71
27 15 0.29
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (26 bp):
AAGGAAAATAAGAATAAAAAGCTCTT
Found at i:46139 original size:20 final size:20
Alignment explanation
Indices: 46081--46159 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
46071 CTGTTCATGG
*
46081 TATCGATACTACTGTACACACAA
1 TATCGATACTA--GT-CATACAA
* * *
46104 TATCGGTATTATTCATACAA
1 TATCGATACTAGTCATACAA
* *
46124 TATCGATACTAGTCATATAG
1 TATCGATACTAGTCATACAA
*
46144 TA-CGATACTATTCATA
1 TATCGATACTAGTCATA
46160 AAAATATTCT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 13 0.28
20 23 0.50
21 1 0.02
23 9 0.20
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (20 bp):
TATCGATACTAGTCATACAA
Found at i:46402 original size:2 final size:2
Alignment explanation
Indices: 46395--46421 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46385 ACAAATATCA
46395 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
46422 ACAACACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46610 original size:29 final size:29
Alignment explanation
Indices: 46578--46669 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 29
46568 GGCACCCAAA
*
46578 TAGAAATTGGATGGGGATATAATCCCATG
1 TAGAAATAGGATGGGGATATAATCCCATG
*** *
46607 TAGAAATAGGACAAGGATATAATCCTATG
1 TAGAAATAGGATGGGGATATAATCCCATG
* * *
46636 TAGAAATAGGGTGGGAAT-TAAATCACATG
1 TAGAAATAGGATGGGGATAT-AATCCCATG
46665 TAGAA
1 TAGAA
46670 TCAGGAATGC
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 1 0.02
29 49 0.98
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (29 bp):
TAGAAATAGGATGGGGATATAATCCCATG
Found at i:51032 original size:2 final size:2
Alignment explanation
Indices: 51027--51063 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
51017 CTCTACAGTA
51027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51064 ACACAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57720 original size:12 final size:11
Alignment explanation
Indices: 57679--57740 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 11
57669 CACTTAATTA
57679 GATAATAATAT
1 GATAATAATAT
57690 G-TAATAATA-
1 GATAATAATAT
57699 GATATTATAATACT
1 GATA--ATAATA-T
57713 GATAATAATA-
1 GATAATAATAT
*
57723 AATAAATAATAT
1 GAT-AATAATAT
57735 -ATAATA
1 GATAATA
57741 TAATATATAG
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
9 1 0.02
10 16 0.37
11 10 0.23
12 12 0.28
14 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (11 bp):
GATAATAATAT
Found at i:57728 original size:4 final size:4
Alignment explanation
Indices: 57719--57805 Score: 56
Period size: 4 Copynumber: 21.8 Consensus size: 4
57709 TACTGATAAT
* * * * * *
57719 AATA AATA AAT- AATA TATA ATATA ATATA TAGA AATA TATA TATA TATA
1 AATA AATA AATA AATA AATA A-ATA A-ATA AATA AATA AATA AATA AATA
57768 AATA AATA AATA AAT- -ATA ACATA AAT- AATA ATATA AAT
1 AATA AATA AATA AATA AATA A-ATA AATA AATA A-ATA AAT
57806 TAAAATATAA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
2 2 0.03
3 6 0.09
4 44 0.65
5 16 0.24
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (4 bp):
AATA
Found at i:57743 original size:35 final size:34
Alignment explanation
Indices: 57679--57745 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
57669 CACTTAATTA
** *
57679 GATAATAATATGTAATAATAGATATTATAATACT
1 GATAATAATAAATAATAATAGATAATATAATACT
*
57713 GATAATAATAAATAAATAATATATAATATAATA
1 GATAATAATAAAT-AATAATAGATAATATAATA
57746 TATAGAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 11 0.39
35 17 0.61
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (34 bp):
GATAATAATAAATAATAATAGATAATATAATACT
Found at i:57745 original size:12 final size:12
Alignment explanation
Indices: 57717--57817 Score: 70
Period size: 12 Copynumber: 8.5 Consensus size: 12
57707 AATACTGATA
*
57717 ATAATAAATAA-
1 ATAATATATAAT
57728 ATAATATATAAT
1 ATAATATATAAT
*
57740 ATAATATATAGAA
1 ATAATATATA-AT
57753 AT-ATATATATAT
1 ATAATATATA-AT
*
57765 ATAAATAAATAA-
1 AT-AATATATAAT
*
57777 ATAA-ATATAAC
1 ATAATATATAAT
57788 ATAA-ATAATAAT
1 ATAATAT-ATAAT
*
57800 ATAA-ATTAAAAT
1 ATAATA-TATAAT
57812 ATAATA
1 ATAATA
57818 ATATTATCTA
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
10 5 0.07
11 18 0.24
12 39 0.53
13 6 0.08
14 6 0.08
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:57831 original size:20 final size:20
Alignment explanation
Indices: 57691--57821 Score: 71
Period size: 20 Copynumber: 6.5 Consensus size: 20
57681 TAATAATATG
* * *
57691 TAATAATAGATATTATAATA
1 TAATAATATAAATTAAAATA
* *
57711 CTGATAATAATAAATAAATAATA
1 -TAATAAT-ATAAATTAA-AATA
57734 T-ATAATATAATATATAGAAATA
1 TAATAATATAA-AT-TA-AAATA
57756 TATATATATATAAA-T-AAATA
1 TA-ATA-ATATAAATTAAAATA
57776 -AATAAATATAACA-T--AA-A
1 TAAT-AATATAA-ATTAAAATA
57793 TAATAATATAAATTAAAATA
1 TAATAATATAAATTAAAATA
57813 TAATAATAT
1 TAATAATAT
57822 TATCTAAAAT
Statistics
Matches: 89, Mismatches: 6, Indels: 31
0.71 0.05 0.25
Matches are distributed among these distances:
16 1 0.01
17 9 0.10
18 13 0.15
19 6 0.07
20 19 0.21
21 13 0.15
22 13 0.15
23 5 0.06
24 4 0.04
25 6 0.07
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
TAATAATATAAATTAAAATA
Found at i:58364 original size:9 final size:10
Alignment explanation
Indices: 58338--58397 Score: 50
Period size: 11 Copynumber: 5.6 Consensus size: 10
58328 TGTAGTACAT
58338 TAAAAAGAAAA
1 TAAAAA-AAAA
58349 -AATAAAAAAA
1 TAA-AAAAAAA
58359 TAAAAAAAAA
1 TAAAAAAAAA
* *
58369 GTCAAAAAAGA
1 -TAAAAAAAAA
58380 TAAAAAATAAAA
1 T-AAAAA-AAAA
58392 TAAAAA
1 TAAAAA
58398 GCCAAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 14 0.35
11 22 0.55
12 4 0.10
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.12
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:58364 original size:21 final size:21
Alignment explanation
Indices: 58338--58397 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
58328 TGTAGTACAT
58338 TAAAAAGAAAAAATAAAAAA-A
1 TAAAAA-AAAAAATAAAAAAGA
*
58359 T-AAAAAAAAAGTCAAAAAAGA
1 TAAAAAAAAAAAT-AAAAAAGA
*
58380 TAAAAAATAAAATAAAAA
1 TAAAAAAAAAAATAAAAA
58398 GCCAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.18
20 10 0.30
21 8 0.24
22 9 0.27
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.12
Consensus pattern (21 bp):
TAAAAAAAAAAATAAAAAAGA
Found at i:58383 original size:29 final size:28
Alignment explanation
Indices: 58345--58414 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
58335 CATTAAAAAG
*
58345 AAAAAATAAAAAAATAAAA-AAAAAGTCA
1 AAAAAAT-AAAAAATAAAATAAAAAGCCA
58373 AAAAAGATAAAAAATAAAATAAAAAGCC-
1 AAAAA-ATAAAAAATAAAATAAAAAGCCA
*
58401 AAAAAATGAAAAAT
1 AAAAAATAAAAAAT
58415 CACATAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 8 0.21
28 21 0.55
29 9 0.24
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (28 bp):
AAAAAATAAAAAATAAAATAAAAAGCCA
Found at i:58385 original size:28 final size:28
Alignment explanation
Indices: 58338--58413 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
58328 TGTAGTACAT
*
58338 TAAAAAG--AAAAAATAAAAAAATAAAA
1 TAAAAAGCCAAAAAAGAAAAAAATAAAA
*
58364 -AAAAAGTCAAAAAAGATAAAAAATAAAA
1 TAAAAAGCCAAAAAAGA-AAAAAATAAAA
58392 TAAAAAGCCAAAAAATGAAAAA
1 TAAAAAGCCAAAAAA-GAAAAA
58414 TCACATAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 6 0.14
27 7 0.16
28 11 0.26
29 17 0.40
30 2 0.05
ACGTcount: A:0.79, C:0.04, G:0.07, T:0.11
Consensus pattern (28 bp):
TAAAAAGCCAAAAAAGAAAAAAATAAAA
Found at i:60290 original size:31 final size:31
Alignment explanation
Indices: 60252--60344 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
60242 ATTTCACTTA
60252 TGGAAGATGATAAGGTTTAGGTGTCTTGGTT
1 TGGAAGATGATAAGGTTTAGGTGTCTTGGTT
60283 TGGAAGATGATAAGGTTTAGGTGTCTTGGTT
1 TGGAAGATGATAAGGTTTAGGTGTCTTGGTT
* *
60314 TGGAAGATAATAAGG-TTAGATGTCTTGGTT
1 TGGAAGATGATAAGGTTTAGGTGTCTTGGTT
60344 T
1 T
60345 AATGGTAATT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
30 15 0.25
31 45 0.75
ACGTcount: A:0.25, C:0.03, G:0.33, T:0.39
Consensus pattern (31 bp):
TGGAAGATGATAAGGTTTAGGTGTCTTGGTT
Found at i:65817 original size:59 final size:59
Alignment explanation
Indices: 65733--66011 Score: 477
Period size: 59 Copynumber: 4.7 Consensus size: 59
65723 GTGGCACTAA
65733 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
*
65792 GTGTACTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* *
65851 GTGTGCTAAAATGGTAATGAAATCATACTAAGTGTATGAATTTCCAGATATGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * *
65910 TTGTGCTAAAATGGTAAGGAAATCATACAAAGTGTATGAATTTCCAGATATGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * *
65969 GTGTGCTAAACTGTTAAGGAATTCATACTAAGTGTATGAATTT
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTT
66012 TCGAAATGGG
Statistics
Matches: 208, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 208 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (59 bp):
GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
Found at i:67932 original size:30 final size:31
Alignment explanation
Indices: 67875--67936 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
67865 ATTTCACTTA
67875 TGGAAGATGATAAGGTTTAGGTATCTTGGTT
1 TGGAAGATGATAAGGTTTAGGTATCTTGGTT
*
67906 TGGAAGATGATAAGG-TTAGGTGTCTTGGTT
1 TGGAAGATGATAAGGTTTAGGTATCTTGGTT
67936 T
1 T
67937 AATGGTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.24, C:0.03, G:0.34, T:0.39
Consensus pattern (31 bp):
TGGAAGATGATAAGGTTTAGGTATCTTGGTT
Found at i:69592 original size:40 final size:40
Alignment explanation
Indices: 69543--69652 Score: 175
Period size: 40 Copynumber: 2.7 Consensus size: 40
69533 AGGACACTAA
69543 GTGTAATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGT-ATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* * *
69584 GTGTATATGGTGGGAACGACCTTATGTGTAATGCACTTTG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
*
69624 GTGTATATGGTGGGCATGACCTTATGTGT
1 GTGTATATGGTGGGCACGACCTTATGTGT
69653 TGCACTACGG
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
40 60 0.94
41 4 0.06
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:70996 original size:24 final size:26
Alignment explanation
Indices: 70969--71053 Score: 66
Period size: 26 Copynumber: 3.1 Consensus size: 26
70959 ATTTTTATTT
70969 TAATAATATATAATAAAT-TA-TTAA
1 TAATAATATATAATAAATATATTTAA
* **
70993 TAATGAATAATATTATTTATATATTTAA
1 TAAT-AAT-ATATAATAAATATATTTAA
*
71021 TAATAATATTATAATCTAAAAATATTTTAA
1 TAATAATA-TATAA--TAAATATA-TTTAA
71051 TAA
1 TAA
71054 AGATAATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
24 4 0.09
25 3 0.07
26 9 0.20
27 9 0.20
28 8 0.17
29 5 0.11
30 8 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (26 bp):
TAATAATATATAATAAATATATTTAA
Found at i:71022 original size:21 final size:20
Alignment explanation
Indices: 70974--71046 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 20
70964 TATTTTAATA
*
70974 ATATATAATAA-ATTATTA-
1 ATATTTAATAATATTATTAT
* *
70992 ATAATGAATAATATTATTTAT
1 ATATTTAATAATATTA-TTAT
*
71013 ATATTTAATAATAATATTAT
1 ATATTTAATAATATTATTAT
* *
71033 A-ATCTAAAAATATT
1 ATATTTAATAATATT
71047 TTAATAAAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 8 0.19
19 14 0.33
20 8 0.19
21 13 0.30
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (20 bp):
ATATTTAATAATATTATTAT
Found at i:71225 original size:27 final size:28
Alignment explanation
Indices: 71187--71240 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
71177 AAATTATAAA
*
71187 ATTAATATTTTAATAATAAATAA-ATTAT
1 ATTAATATTTTAAAAAT-AATAATATTAT
71215 ATTAATA-TTTAAAAATAATAATATTA
1 ATTAATATTTTAAAAATAATAATATTA
71241 AGTTTTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 12 0.50
28 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTAATATTTTAAAAATAATAATATTAT
Found at i:71247 original size:22 final size:23
Alignment explanation
Indices: 71204--71262 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
71194 TTTTAATAAT
*
71204 AAATAAATTATATTAATATTTAA
1 AAATAAATAATATTAATATTTAA
71227 AAAT-AATAATATTAAGT-TTT-A
1 AAATAAATAATATTAA-TATTTAA
**
71248 TGATAAATAATATTA
1 AAATAAATAATATTA
71263 TTTATTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 3 0.10
22 23 0.74
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
AAATAAATAATATTAATATTTAA
Found at i:73448 original size:8 final size:8
Alignment explanation
Indices: 73425--73459 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
73415 CAACCACGGT
73425 TGAACCCAG
1 TGAA-CCAG
73434 TTGAACCAG
1 -TGAACCAG
73443 TGAACCAG
1 TGAACCAG
73451 TGAACCAG
1 TGAACCAG
73459 T
1 T
73460 ACCTTCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 4 0.16
10 4 0.16
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (8 bp):
TGAACCAG
Found at i:79361 original size:105 final size:105
Alignment explanation
Indices: 79177--79382 Score: 268
Period size: 105 Copynumber: 2.0 Consensus size: 105
79167 CCAACTCAGT
* * * *
79177 ATCCTCAGCTGCACTAACTAAGGTTGCACCATCAACCTCTTGTTGAACTGCTGCTCCTAGAGAAG
1 ATCCTCAGCTGCACTAAATAAGGTTGCACCAGCAACCTCTTGCTGAACTGCTGCTCCCAGAGAAG
* * * **
79242 TAACACCCATATCCATAGTAGCTTGACTTATCTCACTATA
66 TAACACCCACATCCACAGTAGCCTGACCCATCTCACTATA
* * * * * *
79282 ATCCTCAGTTGCATTAAATGAGGTTGCACTAGCTACCTCTTGCTGAACTGTTGCTCCCAGAGAAG
1 ATCCTCAGCTGCACTAAATAAGGTTGCACCAGCAACCTCTTGCTGAACTGCTGCTCCCAGAGAAG
*
79347 TAACACCCGCATCCACAGTAGCCTGACCCATCTCAC
66 TAACACCCACATCCACAGTAGCCTGACCCATCTCAC
79383 CAGAAAAATG
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
105 85 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (105 bp):
ATCCTCAGCTGCACTAAATAAGGTTGCACCAGCAACCTCTTGCTGAACTGCTGCTCCCAGAGAAG
TAACACCCACATCCACAGTAGCCTGACCCATCTCACTATA
Found at i:85605 original size:23 final size:22
Alignment explanation
Indices: 85571--85614 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
85561 ATTATTTTCT
*
85571 AACTTATAATGAAGTATAAAATA
1 AACTTATAATG-AGAATAAAATA
85594 AACTTGAT-ATGAGAATAAAAT
1 AACTT-ATAATGAGAATAAAAT
85615 GGCATAGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 8 0.42
24 2 0.11
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (22 bp):
AACTTATAATGAGAATAAAATA
Found at i:89854 original size:2 final size:2
Alignment explanation
Indices: 89847--89872 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89837 TCTATTTTAG
89847 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
89873 AATCATACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92905 original size:26 final size:27
Alignment explanation
Indices: 92864--92915 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
92854 ACTTAGGTTA
** *
92864 GGTAAAATTATGAAAA-CCCCTTATGG
1 GGTAAAATTACAAAAATACCCTTATGG
92890 GGTAAAATTACAAAAATACCCTTATG
1 GGTAAAATTACAAAAATACCCTTATG
92916 TTGTAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (27 bp):
GGTAAAATTACAAAAATACCCTTATGG
Found at i:96564 original size:17 final size:17
Alignment explanation
Indices: 96521--96565 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
96511 CCTTAAATCT
**
96521 TTTCTTCTACATTTCCA
1 TTTCTTCTATTTTTCCA
96538 TTTCTTCTATTTTTCCA
1 TTTCTTCTATTTTTCCA
96555 TTTCTTCTATT
1 TTTCTTCTATT
96566 CCTTTCTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTCTTCTATTTTTCCA
Found at i:100707 original size:2 final size:2
Alignment explanation
Indices: 100700--100735 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
100690 AGTTATTTTC
*
100700 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
100736 GTTATTATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107004 original size:21 final size:21
Alignment explanation
Indices: 106978--107033 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
106968 TTTTAATGTT
106978 TTAAGCTTATATAAGCTTTCC
1 TTAAGCTTATATAAGCTTTCC
106999 TTAAGCTTATATAAGCTTTCC
1 TTAAGCTTATATAAGCTTTCC
107020 TTAAGCTTATATAA
1 TTAAGCTTATATAA
107034 CACTCAAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (21 bp):
TTAAGCTTATATAAGCTTTCC
Found at i:112456 original size:65 final size:65
Alignment explanation
Indices: 112375--112505 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
112365 TCTCATCCAC
112375 AAGGTAGTCTCCCTAGTGATACTGAGGTCACTAAACATCATGGAAAGGAGCAGCACAGTGTACTT
1 AAGGTAGTCTCCCTAGTGATACTGAGGTCACTAAACATCATGGAAAGGAGCAGCACAGTGTACTT
* * *
112440 AAGGTATTCTCCCTAGTGATATTGAGGTCACTAAACATCATGGAAAGGAGCAGCATAGTGTACTT
1 AAGGTAGTCTCCCTAGTGATACTGAGGTCACTAAACATCATGGAAAGGAGCAGCACAGTGTACTT
112505 A
1 A
112506 CACTAAGGAG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (65 bp):
AAGGTAGTCTCCCTAGTGATACTGAGGTCACTAAACATCATGGAAAGGAGCAGCACAGTGTACTT
Found at i:115538 original size:14 final size:15
Alignment explanation
Indices: 115503--115535 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
115493 CCGAAATACA
115503 GAAATCAGATATCAG
1 GAAATCAGATATCAG
115518 GAAATCA-ATATTCAG
1 GAAATCAGATA-TCAG
115533 GAA
1 GAA
115536 TCACGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAATCAGATATCAG
Found at i:116342 original size:28 final size:30
Alignment explanation
Indices: 116308--116427 Score: 144
Period size: 29 Copynumber: 4.2 Consensus size: 30
116298 AATAATTACT
*
116308 AAAATAGAACC-TTCTCGAATTAAATT-CC
1 AAAATAGAACCATTTTCGAATTAAATTCCC
* *
116336 AAAATAGCACCTTTTTC-AATTAAATTCCC
1 AAAATAGAACCATTTTCGAATTAAATTCCC
* *
116365 AAAATAGCA-CTTTTTCGAATTAAATTCCC
1 AAAATAGAACCATTTTCGAATTAAATTCCC
116394 AAAATAGAACCCA-TTTCGAATT-AATTCCC
1 AAAATAGAA-CCATTTTCGAATTAAATTCCC
116423 AAAAT
1 AAAAT
116428 GTCACCGAGT
Statistics
Matches: 83, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
28 26 0.31
29 47 0.57
30 9 0.11
31 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (30 bp):
AAAATAGAACCATTTTCGAATTAAATTCCC
Found at i:116424 original size:58 final size:57
Alignment explanation
Indices: 116308--116427 Score: 161
Period size: 58 Copynumber: 2.1 Consensus size: 57
116298 AATAATTACT
* **
116308 AAAATAGAACCTTCTCGAATTAAATTCCAAAATAGCACCTTTTTCAATTAAATTCCC
1 AAAATAGAACCTTCTCGAATTAAATTCCAAAATAGAACCCATTTCAATTAAATTCCC
* * *
116365 AAAATAGCACTTTTTCGAATTAAATTCCCAAAATAGAACCCATTTCGAATT-AATTCCC
1 AAAATAGAACCTTCTCGAATTAAATT-CCAAAATAGAACCCATTTC-AATTAAATTCCC
116423 AAAAT
1 AAAAT
116428 GTCACCGAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 23 0.42
58 28 0.51
59 4 0.07
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (57 bp):
AAAATAGAACCTTCTCGAATTAAATTCCAAAATAGAACCCATTTCAATTAAATTCCC
Found at i:123393 original size:29 final size:29
Alignment explanation
Indices: 123361--123500 Score: 147
Period size: 29 Copynumber: 4.8 Consensus size: 29
123351 AATAATTACT
** *
123361 AAAATAGTGCCTTTTCGAATTAAATTCCC
1 AAAATAGCACCTTTTCAAATTAAATTCCC
* *
123390 AAAACAACACCTTTTCAAATTAAATTCCC
1 AAAATAGCACCTTTTCAAATTAAATTCCC
* ** *
123419 AATATAGCACCTTTTTGAATCAAATTCCC
1 AAAATAGCACCTTTTCAAATTAAATTCCC
* *
123448 AAAATATCACCCATTTCAAATT-AATTCCC
1 AAAATAGCA-CCTTTTCAAATTAAATTCCC
*
123477 AAAATAGCACCCATTTCAAATTAA
1 AAAATAGCA-CCTTTTCAAATTAA
123501 TTATCAAAAT
Statistics
Matches: 91, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
29 82 0.90
30 9 0.10
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAATAGCACCTTTTCAAATTAAATTCCC
Found at i:123444 original size:58 final size:58
Alignment explanation
Indices: 123361--123487 Score: 166
Period size: 58 Copynumber: 2.2 Consensus size: 58
123351 AATAATTACT
** * *
123361 AAAATAGTGCCTTTTCGAATTAAATTCCCAAAACAACA-CCTTTTCAAATTAAATTCCC
1 AAAATAGCACCTTTTCGAATCAAATTCCCAAAACAACACCCATTTCAAATT-AATTCCC
* * * *
123419 AATATAGCACCTTTTTGAATCAAATTCCCAAAATATCACCCATTTCAAATTAATTCCC
1 AAAATAGCACCTTTTCGAATCAAATTCCCAAAACAACACCCATTTCAAATTAATTCCC
123477 AAAATAGCACC
1 AAAATAGCACC
123488 CATTTCAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 48 0.81
59 11 0.19
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (58 bp):
AAAATAGCACCTTTTCGAATCAAATTCCCAAAACAACACCCATTTCAAATTAATTCCC
Found at i:123508 original size:29 final size:29
Alignment explanation
Indices: 123441--123510 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
123431 TTTTGAATCA
* *
123441 AATTCCCAAAATATCACCCATTTCAAATT
1 AATTACCAAAATAGCACCCATTTCAAATT
*
123470 AATTCCCAAAATAGCACCCATTTCAAATT
1 AATTACCAAAATAGCACCCATTTCAAATT
*
123499 AATTATCAAAAT
1 AATTACCAAAAT
123511 GTCACCCGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.30
Consensus pattern (29 bp):
AATTACCAAAATAGCACCCATTTCAAATT
Found at i:123509 original size:58 final size:59
Alignment explanation
Indices: 123402--123517 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 59
123392 AACAACACCT
* * ** *
123402 TTTCAAATTAAATTCCCAATATAGCACCTTTTTGAATCAAATTCCCAAAATATCACCCA
1 TTTCAAATTAAATTCCCAAAATAGCACCATTTCAAATCAAATTACCAAAATATCACCCA
* * *
123461 TTTCAAATT-AATTCCCAAAATAGCACCCATTTCAAAT-TAATTATCAAAATGTCACCC
1 TTTCAAATTAAATTCCCAAAATAGCA-CCATTTCAAATCAAATTACCAAAATATCACCC
123518 GGTCAACGGT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
58 31 0.65
59 17 0.35
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (59 bp):
TTTCAAATTAAATTCCCAAAATAGCACCATTTCAAATCAAATTACCAAAATATCACCCA
Found at i:125462 original size:46 final size:46
Alignment explanation
Indices: 125376--125685 Score: 442
Period size: 46 Copynumber: 6.7 Consensus size: 46
125366 TTTAAATTAA
* * * *
125376 GGCATCCTTTCATGCCTTAAATGCATCATTCCATGTATTTTAATTAT
1 GGCATCCTTTCATGCCTT-AATGCATCCTTTCATGCATTTTAGTTAT
* * *
125423 GGAATCCTTTCATGCCTTAATGCATCCTTTCATTCATTTTAGAT-T
1 GGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
* *
125468 GGCATCCTTTCATACCTTAATGAATCCTTTCATGCATTTTAGTTAT
1 GGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
* *
125514 GACATCCTTACATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
1 GGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
* * * *
125560 GGCATCTTTTTATTCCTTAATGCATTCTTTCATGCATTTTAGTTAT
1 GGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
*
125606 GGCATCCTTTCATCCCTTAATGCATCCTTTCATGCATTTTAGTTAT
1 GGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
* *
125652 GGCATCCTTTCATGCCCTAATGCATTCTTTCATG
1 GGCATCCTTTCATGCCTTAATGCATCCTTTCATG
125686 TCTTAATGTA
Statistics
Matches: 233, Mismatches: 29, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
45 40 0.17
46 176 0.76
47 17 0.07
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (46 bp):
GGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
Found at i:125522 original size:26 final size:25
Alignment explanation
Indices: 125442--125666 Score: 132
Period size: 26 Copynumber: 9.6 Consensus size: 25
125432 TCATGCCTTA
*
125442 ATGCATCCTTTCATTCATTTTAGATT
1 ATGCATCCTTTCATGCATTTTAG-TT
* **
125468 -GGCATCCTTTCAT--ACCTTA---
1 ATGCATCCTTTCATGCATTTTAGTT
*
125487 ATGAATCCTTTCATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
* *
125512 ATGACATCCTTACATGC--CTTA---
1 ATG-CATCCTTTCATGCATTTTAGTT
125533 ATGCATCCTTTCATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
* * * *
125558 ATGGCATCTTTTTATTC--CTTA---
1 AT-GCATCCTTTCATGCATTTTAGTT
*
125579 ATGCATTCTTTCATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
**
125604 ATGGCATCCTTTCAT-C-CCTTA---
1 AT-GCATCCTTTCATGCATTTTAGTT
125625 ATGCATCCTTTCATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
125650 ATGGCATCCTTTCATGC
1 AT-GCATCCTTTCATGC
125667 CCTAATGCAT
Statistics
Matches: 148, Mismatches: 26, Indels: 50
0.66 0.12 0.22
Matches are distributed among these distances:
20 45 0.30
21 8 0.05
22 13 0.09
23 4 0.03
24 9 0.06
25 22 0.15
26 47 0.32
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (25 bp):
ATGCATCCTTTCATGCATTTTAGTT
Found at i:126620 original size:14 final size:14
Alignment explanation
Indices: 126572--126628 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
126562 TTAACCCGAC
*
126572 CGAGTCAACTCAGTC
1 CGAGTCAACTC-GTT
*
126587 CGAGTCAAATCG-T
1 CGAGTCAACTCGTT
*
126600 CTAAGTCAACTCGTT
1 C-GAGTCAACTCGTT
*
126615 CGAGTCAACCCGTT
1 CGAGTCAACTCGTT
126629 GACTTTGACC
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
13 1 0.03
14 21 0.62
15 12 0.35
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (14 bp):
CGAGTCAACTCGTT
Found at i:135037 original size:17 final size:16
Alignment explanation
Indices: 135015--135057 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
135005 GTTTTTCAAC
135015 TTTTTCTTTCTTTTCTT
1 TTTTTCTTTCTTTT-TT
135032 TTTTTC-TTCTTTTTT
1 TTTTTCTTTCTTTTTT
135047 TCTTCTTCTTT
1 T-TT-TTCTTT
135058 TGAGTGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.13
16 9 0.39
17 9 0.39
18 2 0.09
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTCTTTTTT
Found at i:135043 original size:11 final size:11
Alignment explanation
Indices: 135027--135058 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
135017 TTTCTTTCTT
135027 TTCTTTTTTTC
1 TTCTTTTTTTC
135038 TTCTTTTTTTC
1 TTCTTTTTTTC
135049 TTCTTCTTTT
1 TTCTT-TTTT
135059 GAGTGCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:135047 original size:14 final size:14
Alignment explanation
Indices: 135015--135058 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
135005 GTTTTTCAAC
*
135015 TTTTTCTTTCTT-T
1 TTTTTTTTTCTTCT
*
135028 TCTTTTTTTCTTCT
1 TTTTTTTTTCTTCT
*
135042 TTTTTTCTTCTTCT
1 TTTTTTTTTCTTCT
135056 TTT
1 TTT
135059 GAGTGCTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTCTTCT
Found at i:142367 original size:16 final size:16
Alignment explanation
Indices: 142343--142386 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
142333 TTTGTTTTTT
142343 TTTTC-TCTTTTTTCA
1 TTTTCTTCTTTTTTCA
142358 TTTTCTTCTTTTTTCA
1 TTTTCTTCTTTTTTCA
142374 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
142387 GTTTTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTCTTTTTTCA
Found at i:142371 original size:30 final size:28
Alignment explanation
Indices: 142337--142426 Score: 78
Period size: 30 Copynumber: 3.1 Consensus size: 28
142327 TTTCACTTTG
142337 TTTTTTTTTTCTCTTTTTTCATTTTCTTCT
1 TTTTTTTTTTCT-TTTTTTC-TTTTCTTCT
* *
142367 TTTTTCATTTTCTTCTTTTTGTTTTCTT-T
1 TTTTT-TTTTTCTT-TTTTTCTTTTCTTCT
*
142396 TTTTTTTATCTT-TTTCTTTCTTTT-TTCT
1 TTTTTTT-T-TTCTTTTTTTCTTTTCTTCT
142424 TTT
1 TTT
142427 GTGGCTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
27 2 0.04
28 13 0.26
29 9 0.18
30 15 0.30
31 11 0.22
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.81
Consensus pattern (28 bp):
TTTTTTTTTTCTTTTTTTCTTTTCTTCT
Found at i:142377 original size:24 final size:23
Alignment explanation
Indices: 142342--142426 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 23
142332 CTTTGTTTTT
*
142342 TTTTTCTCTTTTTTCATTTTCTTC
1 TTTTT-TCTTTTTTCTTTTTCTTC
*
142366 TTTTTTCATTTTCTTCTTTTTGTTTTC
1 TTTTTTC-TTTT-TTC-TTTT-TCTTC
*
142393 TTTTTT-TTTTATCTTTTTCTTTC
1 TTTTTTCTTTTTTCTTTTTC-TTC
142416 TTTTTTCTTTT
1 TTTTTTCTTTT
142427 GTGGCTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
22 1 0.02
23 15 0.29
24 15 0.29
25 7 0.14
26 3 0.06
27 10 0.20
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.80
Consensus pattern (23 bp):
TTTTTTCTTTTTTCTTTTTCTTC
Found at i:142393 original size:27 final size:24
Alignment explanation
Indices: 142380--142426 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
142370 TTCATTTTCT
*
142380 TCTTTTTGTTTTCTTTTTT-TTTTA
1 TCTTTTT-CTTTCTTTTTTCTTTTA
142404 TCTTTTTCTTTCTTTTTTCTTTT
1 TCTTTTTCTTTCTTTTTTCTTTT
142427 GTGGCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (24 bp):
TCTTTTTCTTTCTTTTTTCTTTTA
Found at i:142409 original size:7 final size:6
Alignment explanation
Indices: 142337--142426 Score: 51
Period size: 6 Copynumber: 14.7 Consensus size: 6
142327 TTTCACTTTG
* * * * *
142337 TTTTTT TTTTCTC TTTTTTC ATTTTC -TTCT- TTTTTC ATTTTC TTCTTTT
1 TTTTTC TTTT-TC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC
* *
142386 TGTTTTC TTTTTT TTTTATC TTTTTC TTTCT- TTTTTC TTTT
1 T-TTTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC TTTT
142427 GTGGCTTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
5 10 0.16
6 33 0.52
7 16 0.25
8 5 0.08
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:143112 original size:14 final size:14
Alignment explanation
Indices: 143093--143122 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
143083 CCCCTTTTCA
*
143093 TTTTTCTTTTTCTT
1 TTTTTCTTTTCCTT
143107 TTTTTCTTTTCCTT
1 TTTTTCTTTTCCTT
143121 TT
1 TT
143123 ATTTTTGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTTTTCCTT
Found at i:143116 original size:19 final size:19
Alignment explanation
Indices: 143094--143134 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
143084 CCCTTTTCAT
* * *
143094 TTTTCTTTTTCTTTTTTTC
1 TTTTCCTTTTATTTTTGTC
143113 TTTTCCTTTTATTTTTGTC
1 TTTTCCTTTTATTTTTGTC
143132 TTT
1 TTT
143135 ATTTGTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTCCTTTTATTTTTGTC
Found at i:147208 original size:14 final size:15
Alignment explanation
Indices: 147183--147220 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
147173 AAAGCAACAA
147183 AAAGAGAAAAAGAAAG
1 AAAGA-AAAAAGAAAG
147199 AAA-AAAAAAGAAAG
1 AAAGAAAAAAGAAAG
147213 AAAGAAAA
1 AAAGAAAA
147221 GACTCCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.62
15 5 0.24
16 3 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAAAG
Found at i:151243 original size:13 final size:13
Alignment explanation
Indices: 151225--151249 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
151215 ACTATCTGTT
151225 CATCACCATTTTC
1 CATCACCATTTTC
151238 CATCACCATTTT
1 CATCACCATTTT
151250 TCACGCCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:166293 original size:20 final size:19
Alignment explanation
Indices: 166268--166307 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
166258 TCTTCTAGAA
166268 ATCGATCTGAGTCAACTCTG
1 ATCGATCTGAGTCAAC-CTG
166288 ATCGATCTGAGTCAACCTG
1 ATCGATCTGAGTCAACCTG
166307 A
1 A
166308 ACTTGCTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (19 bp):
ATCGATCTGAGTCAACCTG
Found at i:166451 original size:22 final size:21
Alignment explanation
Indices: 166394--166458 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
166384 CCTATTGACA
*
166394 TGACCGTTGACTTTACCATAAT
1 TGACTGTTGACTTTACCA-AAT
* *
166416 TGACT-TAGATCTTTAACCAATT
1 TGACTGTTGA-CTTT-ACCAAAT
166438 TGACTGTTGACTTTGACCAAA
1 TGACTGTTGACTTT-ACCAAA
166459 AAGTTAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.09
22 24 0.71
23 7 0.21
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (21 bp):
TGACTGTTGACTTTACCAAAT
Found at i:171151 original size:12 final size:12
Alignment explanation
Indices: 171134--171161 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
171124 ATTTTTCATA
171134 AAAAAATAAAAT
1 AAAAAATAAAAT
171146 AAAAAATAAAAT
1 AAAAAATAAAAT
171158 AAAA
1 AAAA
171162 TAAAAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:171768 original size:16 final size:16
Alignment explanation
Indices: 171733--171768 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
171723 GCCAGGCCAG
*
171733 GCCAGGCTTTATATAG
1 GCCAGGCTTTATATAA
*
171749 GCCAGGCTTTATGTAA
1 GCCAGGCTTTATATAA
171765 GCCA
1 GCCA
171769 AGTTGTAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (16 bp):
GCCAGGCTTTATATAA
Found at i:177050 original size:19 final size:20
Alignment explanation
Indices: 177012--177054 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
177002 GAAACCCCTT
*
177012 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
177032 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
177051 TGAA
1 TGAA
177055 GATAAATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:177933 original size:21 final size:20
Alignment explanation
Indices: 177900--177941 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
177890 TTAAAGCTAG
177900 TGAGCTAATATAAACATAACA
1 TGAGCTAATAT-AACATAACA
*
177921 TGAGCTAGA-ATAACATGACA
1 TGAGCTA-ATATAACATAACA
177941 T
1 T
177942 CAGTTAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 9 0.47
22 1 0.05
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (20 bp):
TGAGCTAATATAACATAACA
Found at i:180569 original size:19 final size:20
Alignment explanation
Indices: 180515--180570 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 20
180505 TTTGAACTTC
180515 TTTTTCTTTTCTTCTTTTCTGA
1 TTTTTCTTTTC--CTTTTCTGA
*
180537 TTTTTCTCTT-CTTTT-TG-
1 TTTTTCTTTTCCTTTTCTGA
180554 TCTTTTCTTTTCCTTTT
1 T-TTTTCTTTTCCTTTT
180571 GCACTCTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 1 0.03
18 10 0.33
19 10 0.33
22 9 0.30
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTTCTTTTCCTTTTCTGA
Found at i:181314 original size:19 final size:20
Alignment explanation
Indices: 181276--181318 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
181266 GAAACCCCTT
*
181276 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
181296 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
181315 TGAA
1 TGAA
181319 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:184706 original size:4 final size:4
Alignment explanation
Indices: 184697--184939 Score: 57
Period size: 4 Copynumber: 61.5 Consensus size: 4
184687 AAAAGGTAAG
* * *
184697 AAAT AAAT AAAT AAAT AAAT -AA- AAAT TAAG AAA- AAAC AAATT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT
* * * * * * *
184743 AAA- AGAT AAGAT AAAG AAAG AAA- AGAT AAAAT AAGT AAAAT AAAG AAAA
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT
* * * *
184792 AAAT ATAAA AAAT AAAG AAA- AAA- GAAG AAAT AAAT --AT AAAT AAA-
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * * *
184836 ATAAT AAAA AAAGGT AAAA ATAAT ATAT ATAT ATAT ATAAT AAAT AAA-
1 A-AAT AAAT AAA--T AAAT A-AAT AAAT AAAT AAAT A-AAT AAAT AAAT
* * * * *
184884 AACAT AAA- AAAT -AGT AAAT ATAT ATAT AAAT TAAT AAAAT AGAT -AAT
1 AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT
184931 AAA- AAAT AA
1 AAAT AAAT AA
184940 CATATATATA
Statistics
Matches: 179, Mismatches: 34, Indels: 52
0.68 0.13 0.20
Matches are distributed among these distances:
2 2 0.01
3 29 0.16
4 117 0.65
5 28 0.16
6 3 0.02
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:184762 original size:15 final size:15
Alignment explanation
Indices: 184744--184790 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
184734 AAATTAAATA
184744 AAAGATAAGATAAAG
1 AAAGATAAGATAAAG
*
184759 AAAGAAAAGATAAA-
1 AAAGATAAGATAAAG
*
184773 ATAAG-TAAAATAAAG
1 A-AAGATAAGATAAAG
184788 AAA
1 AAA
184791 AAAATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (15 bp):
AAAGATAAGATAAAG
Found at i:184885 original size:39 final size:36
Alignment explanation
Indices: 184820--184950 Score: 97
Period size: 39 Copynumber: 3.4 Consensus size: 36
184810 AAAAAGAAGA
* *
184820 AATAA-ATATAAATAAAATAATAAAAAAAGGTAAAAAT
1 AATAATATATATATATAATAAT-AAAAAA-GTAAAAAT
184857 AATATATATATATATATAATAAATAAAAACA-TAAAAAAT
1 AATA-ATATATATATATAAT-AATAAAAA-AGT-AAAAAT
* * *
184896 AGTAA-ATATATATATAAATTAATAAAATAGATAATAAAA
1 AATAATATATATATAT-AA-TAATAAAAAAG-TAA-AAAT
*
184935 AATAACATATATATAT
1 AATAATATATATATAT
184951 GTAATCTAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
37 15 0.19
38 14 0.18
39 34 0.44
40 14 0.18
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (36 bp):
AATAATATATATATATAATAATAAAAAAGTAAAAAT
Found at i:184914 original size:19 final size:19
Alignment explanation
Indices: 184820--184950 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 19
184810 AAAAAGAAGA
*
184820 AATAAATATAAATA-AAAT
1 AATAAATATATATATAAAT
* * ** *
184838 AATAAAAAAAGGTAAAAAT
1 AATAAATATATATATAAAT
*
184857 AATATATATATATATATAAT
1 AATAAATATATATATA-AAT
* * *
184877 AAATAAAAACATA-AAAAAT
1 -AATAAATATATATATAAAT
*
184896 AGTAAATATATATATAAATT
1 AATAAATATATATATAAA-T
* *
184916 AATAAA-ATAGATAATAAAA
1 AATAAATATATAT-ATAAAT
184935 AATAACATATATATAT
1 AATAA-ATATATATAT
184951 GTAATCTAAA
Statistics
Matches: 83, Mismatches: 22, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
18 19 0.23
19 31 0.37
20 19 0.23
21 14 0.17
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (19 bp):
AATAAATATATATATAAAT
Found at i:184933 original size:42 final size:41
Alignment explanation
Indices: 184825--184950 Score: 111
Period size: 43 Copynumber: 3.1 Consensus size: 41
184815 GAAGAAATAA
* *
184825 ATATAAATAAAAT-AATAAAAAAAGGT-AAAAAT--AATATAT
1 ATATAAATATAATAAATAAAAACA--TAAAAAATAAAATATAT
*
184864 ATATATATATAATAAATAAAAACATAAAAAATAGTAAATATAT
1 ATATAAATATAATAAATAAAAACATAAAAAATA--AAATATAT
* * *
184907 ATATAAAT-TAATAAAATAGATA-ATAAAAAATAACATATAT
1 ATATAAATATAAT-AAATAAAAACATAAAAAATAAAATATAT
184947 ATAT
1 ATAT
184951 GTAATCTAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
38 1 0.01
39 17 0.23
40 20 0.27
42 14 0.19
43 21 0.29
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (41 bp):
ATATAAATATAATAAATAAAAACATAAAAAATAAAATATAT
Found at i:185557 original size:37 final size:37
Alignment explanation
Indices: 185507--185615 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
185497 ATGCTTCAGG
* *
185507 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
185544 ATCCTATTTTTAGGAGTTTGAAACCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
185581 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACT
185616 TTAATGCTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:187171 original size:2 final size:2
Alignment explanation
Indices: 187164--187194 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
187154 ACATTTTATG
*
187164 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
187195 CATCCTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:187727 original size:20 final size:20
Alignment explanation
Indices: 187700--187825 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
187690 TATATTTTTG
187700 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
187720 GTATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
187745 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
187766 GCATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
187791 GGCATCCATTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
187812 GCATCATTTCATGC
1 GCATCCTTTCATGC
187826 ATTTTATTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
20 38 0.45
21 5 0.06
22 6 0.07
24 6 0.07
25 5 0.06
26 25 0.29
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:187758 original size:26 final size:25
Alignment explanation
Indices: 187722--187863 Score: 151
Period size: 26 Copynumber: 6.0 Consensus size: 25
187712 GCCTTAATGT
187722 ATCCTTTCATGCATTTTATTTATGAC
1 ATCCTTTCATGCATTTTATTTATG-C
*
187748 ATCCTTTCATGC--CTTA---ATGC
1 ATCCTTTCATGCATTTTATTTATGC
187768 ATCCTTTCATGCATTTTATTTATGGC
1 ATCCTTTCATGCATTTTATTTAT-GC
* *
187794 ATCCATTCATGC--CTTA---ATGC
1 ATCCTTTCATGCATTTTATTTATGC
*
187814 ATCATTTCATGCATTTTATTTATGGC
1 ATCCTTTCATGCATTTTATTTAT-GC
187840 ATCCTTTCATGCATTTTATTTATG
1 ATCCTTTCATGCATTTTATTTATG
187864 TATTTGGTTT
Statistics
Matches: 96, Mismatches: 8, Indels: 25
0.74 0.06 0.19
Matches are distributed among these distances:
20 25 0.26
21 5 0.05
22 6 0.06
24 6 0.06
25 5 0.05
26 49 0.51
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (25 bp):
ATCCTTTCATGCATTTTATTTATGC
Found at i:187759 original size:46 final size:46
Alignment explanation
Indices: 187692--187851 Score: 275
Period size: 46 Copynumber: 3.5 Consensus size: 46
187682 AATTTAATTA
* *
187692 TATTTTTGGCATCCTTTCATGCCTTAATGTATCCTTTCATGCATTT
1 TATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTT
*
187738 TATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTT
1 TATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTT
* *
187784 TATTTATGGCATCCATTCATGCCTTAATGCATCATTTCATGCATTT
1 TATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTT
187830 TATTTATGGCATCCTTTCATGC
1 TATTTATGGCATCCTTTCATGC
187852 ATTTTATTTA
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 107 1.00
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.46
Consensus pattern (46 bp):
TATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTT
Found at i:189155 original size:22 final size:23
Alignment explanation
Indices: 189124--189185 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
189114 ACTAATTGAC
*
189124 TTGACCGTTGAC-CTGACTAGAG
1 TTGACTGTTGACTCTGACTAGAG
* * *
189146 TTTACTGTTGACTTTGACTAGTG
1 TTGACTGTTGACTCTGACTAGAG
*
189169 TTGACT-TTGACTTTGAC
1 TTGACTGTTGACTCTGAC
189186 CAAAAAGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (23 bp):
TTGACTGTTGACTCTGACTAGAG
Found at i:189165 original size:23 final size:22
Alignment explanation
Indices: 189137--189185 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
189127 ACCGTTGACC
*
189137 TGACTAGAGTTTACTGTTGACTT
1 TGACTAGAGTTGACT-TTGACTT
*
189160 TGACTAGTGTTGACTTTGACTT
1 TGACTAGAGTTGACTTTGACTT
189182 TGAC
1 TGAC
189186 CAAAAAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.43
Consensus pattern (22 bp):
TGACTAGAGTTGACTTTGACTT
Found at i:190499 original size:43 final size:43
Alignment explanation
Indices: 190450--190785 Score: 449
Period size: 43 Copynumber: 7.8 Consensus size: 43
190440 GAAAAAATGA
* * *
190450 TAAGGTCTTACCCTTGCACATAACAAAAGAGCCT-GGGAAACTG
1 TAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
* * * *
190493 TAAGGTCTTACCCTTGTACACAACAAAGGAACCTAGAGAAATTG
1 TAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
* *
190537 TAAGGCTTACCCTTGCACATAGCAAAGGAACCTGGGAGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG-GAAACTG
*
190581 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAGCTG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
* *
190624 TAAGGCTTACCCTTGCACACATCAAAGGAACCTGGGGAAGCTG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
* * *
190667 TAAGGCTTACCCTTTCACACAACAAAGGAACATAGGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
* * * *
190710 TATGGCTTACCCTTGCACACATCAAAGGAATCTGAGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
* *
190753 TAAGGCTTACCCTTGCACATAGCAAAGGAACCT
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCT
190786 ACGGTAATGG
Statistics
Matches: 259, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
43 207 0.80
44 52 0.20
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
Found at i:190650 original size:130 final size:129
Alignment explanation
Indices: 190450--190786 Score: 451
Period size: 130 Copynumber: 2.6 Consensus size: 129
190440 GAAAAAATGA
* * * *
190450 TAAGGTCTTACCCTTGCACATAACAAAAGAGCCT-GGGAAACTGTAAGGTCTTACCCTTGTACAC
1 TAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGG-CTTACCCTTGCACAC
* * * * *
190514 AACAAAGGAACCTAGAGAAATTGTAAGGCTTACCCTTGCACATAGCAAAGGAACCTGGGAGAAAC
64 AACAAAGGAACCTAGAGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACATAGG-GAAAC
190579 TG
128 TG
* *
190581 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAGCTGTAAGGCTTACCCTTGCACACAT
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAA
* * * *
190646 CAAAGGAACCTGGGGAAGCTGTAAGGCTTACCCTTTCACACAACAAAGGAACATAGGGAAACTG
66 CAAAGGAACCTAGAGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACATAGGGAAACTG
* * * * * *
190710 TATGGCTTACCCTTGCACACATCAAAGGAATCTGAGGAAACTGTAAGGCTTACCCTTGCACATAG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAA
190775 CAAAGGAACCTA
66 CAAAGGAACCTA
190787 CGGTAATGGT
Statistics
Matches: 182, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
129 76 0.42
130 88 0.48
131 18 0.10
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (129 bp):
TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAA
CAAAGGAACCTAGAGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACATAGGGAAACTG
Found at i:193251 original size:21 final size:21
Alignment explanation
Indices: 193227--193272 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
193217 GAAATTTCAT
**
193227 AAAAAACTGAGCTTAATTACG
1 AAAAAACAAAGCTTAATTACG
193248 -AAAAACAAAGCTTAATTACG
1 AAAAAACAAAGCTTAATTACG
193268 AAAAA
1 AAAAA
193273 TGAATCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.20
Consensus pattern (21 bp):
AAAAAACAAAGCTTAATTACG
Found at i:193570 original size:30 final size:30
Alignment explanation
Indices: 193536--193608 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
193526 CGACTTTTTG
*
193536 GTCAAAGTCAACGGTCAATGGGTTGACTCA
1 GTCAAAGTCAACGGTCAACGGGTTGACTCA
* *
193566 GTCAAAGTCAACGGTCAACGGGTTTACTCG
1 GTCAAAGTCAACGGTCAACGGGTTGACTCA
193596 GTCAAAGTCAACG
1 GTCAAAGTCAACG
193609 AGTTGACCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (30 bp):
GTCAAAGTCAACGGTCAACGGGTTGACTCA
Found at i:193686 original size:18 final size:19
Alignment explanation
Indices: 193656--193692 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
193646 ACGCAAGTTG
*
193656 ACTCAGTCGGCTTGGCTCA
1 ACTCAGTCGGCTTAGCTCA
193675 ACTCAG-CGGCTTAGCTCA
1 ACTCAGTCGGCTTAGCTCA
193693 GTGGCTCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.19, C:0.32, G:0.24, T:0.24
Consensus pattern (19 bp):
ACTCAGTCGGCTTAGCTCA
Found at i:197113 original size:139 final size:136
Alignment explanation
Indices: 196777--197200 Score: 473
Period size: 138 Copynumber: 3.1 Consensus size: 136
196767 TCAATAATTG
* ** *
196777 ATTAAAATTAGAGCCTTTATCTTAGGCCTAATTCCACATTTAGTCCTTAAATTAGGTGAGTTCTT
1 ATTAATATTAGAGCCTCCATCTTAGGCCTAATT-CACATTTAGTCCTTAAATTAGGTGAATTCTT
* * * * * *
196842 AATTTGGTCCTCGCTTTTGCTCAAGGTTCCAATTTAATTATTCAAATCGCATAATTGATTAAAAT
65 AATTTGGTCCTTGCTTTTGCTCGA-GTTCCAATTTAATTATTCGAATCACATAATTTATTTAAAT
196907 TAATTA-A
129 TAATTAGA
* * * *
196914 TTTTAATATTAGAGCCTCCAACTTAGGCCCAATTTCACATTTATTCCTTAAATTAGGTGAATTCT
1 -ATTAATATTAGAGCCTCCATCTTAGGCCTAA-TTCACATTTAGTCCTTAAATTAGGTGAATTCT
* *
196979 TAATTTGGTCCTTGGTTTTGCTTGATGTTCCAATTTAATTATTCGAATCACATAATTTATTTAAA
64 TAATTTGGTCCTTGCTTTTGCTCGA-GTTCCAATTTAATTATTCGAATCACATAATTTATTTAAA
*
197044 TTCAACTAGA
128 TT-AATTAGA
** *
197054 ATTAATATTAGAGCCTCCATCTTAGGCCTAACTTCGTATTTAGTCCTTAAATTAGGTGAATTATT
1 ATTAATATTAGAGCCTCCATCTTAGGCCTAA-TTCACATTTAGTCCTTAAATTAGGTGAATTCTT
** * * * *
197119 --TTTTTTTCTT-TTTTTG-TCGAGTTTCCACTTTAATTATTCGAATCACATAA-TTATTTAATT
65 AATTTGGTCCTTGCTTTTGCTCGAG-TTCCAATTTAATTATTCGAATCACATAATTTATTTAA-A
*
197179 TTAATTAGG
128 TTAATTAGA
*
197188 ATTATTATTAGAG
1 ATTAATATTAGAG
197201 TCTGAACTTT
Statistics
Matches: 245, Mismatches: 36, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
134 26 0.11
135 32 0.13
136 5 0.02
137 7 0.03
138 111 0.45
139 63 0.26
140 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (136 bp):
ATTAATATTAGAGCCTCCATCTTAGGCCTAATTCACATTTAGTCCTTAAATTAGGTGAATTCTTA
ATTTGGTCCTTGCTTTTGCTCGAGTTCCAATTTAATTATTCGAATCACATAATTTATTTAAATTA
ATTAGA
Found at i:199658 original size:20 final size:21
Alignment explanation
Indices: 199618--199671 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
199608 TTTTTGAGTG
199618 ATTT-AAT-TTTTATTTGTATT
1 ATTTGAATATTTT-TTTGTATT
**
199638 ATTTTTATATTTTTTTG-ATT
1 ATTTGAATATTTTTTTGTATT
199658 ATTTGAATATTTTT
1 ATTTGAATATTTTT
199672 GTATTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 19 0.66
21 6 0.21
22 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (21 bp):
ATTTGAATATTTTTTTGTATT
Found at i:205305 original size:21 final size:21
Alignment explanation
Indices: 205281--205392 Score: 99
Period size: 21 Copynumber: 5.4 Consensus size: 21
205271 GATTCAATCA
*
205281 GTATCGCTACAATGGTAAGGG
1 GTATCGATACAATGGTAAGGG
* *
205302 GTATTGATACAATGGTAAGGT
1 GTATCGATACAATGGTAAGGG
205323 GTATCGATAC--T-GTAAGGGG
1 GTATCGATACAATGGTAA-GGG
* * *
205342 GTATCGGTACCATAGT-AGGG
1 GTATCGATACAATGGTAAGGG
*
205362 TAGTATCGATACCATGGTAA-GG
1 --GTATCGATACAATGGTAAGGG
205384 GTATCGATA
1 GTATCGATA
205393 TCAGGCAACA
Statistics
Matches: 76, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.05
19 12 0.16
20 12 0.16
21 29 0.38
22 18 0.24
23 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (21 bp):
GTATCGATACAATGGTAAGGG
Found at i:205923 original size:47 final size:47
Alignment explanation
Indices: 205870--206104 Score: 355
Period size: 47 Copynumber: 5.0 Consensus size: 47
205860 AAATCAAATT
* *
205870 CATAATTGAAAATGCATGAAAGTATGGATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
205917 CATAATTGAAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * *
205964 CATAATTAAAAATGCACGAAAGGTTGCATTAAGGCATGAACA-AATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAA-AGGATGC
* * * *
206011 CACAATTGAAAATGAATGAAAGGAAGTATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
206058 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
206105 ATTAAAGCAT
Statistics
Matches: 166, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
46 1 0.01
47 164 0.99
48 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (47 bp):
CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:206096 original size:20 final size:20
Alignment explanation
Indices: 206071--206124 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
206061 AATTGAAAAT
*
206071 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAA
206091 GCATGAAAGGATGCATTAAA
1 GCATGAAAGGATGCATTAAA
*
206111 GCATGAAATGATGC
1 GCATGAAAGGATGC
206125 CATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAA
Found at i:210227 original size:16 final size:16
Alignment explanation
Indices: 210195--210259 Score: 53
Period size: 18 Copynumber: 3.9 Consensus size: 16
210185 ACAAAATTGG
210195 AAAGCAAAAAGAAAAGA
1 AAAGCAAAAAG-AAAGA
*
210212 AAAGACAAAAAGAAGAAAA
1 AAAG-CAAAAAG-A-AAGA
*
210231 AAATCAGAAAA-AAAGA
1 AAAGCA-AAAAGAAAGA
210247 AAAG-AAAAAGAAA
1 AAAGCAAAAAGAAA
210260 TTCAAAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 4 0.10
15 4 0.10
16 6 0.15
17 5 0.12
18 11 0.28
19 10 0.25
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAGCAAAAAGAAAGA
Found at i:210258 original size:19 final size:19
Alignment explanation
Indices: 210200--210259 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
210190 ATTGGAAAGC
*
210200 AAAAAGAAAAGAAAAGACAA
1 AAAAAGAAAAGAAAA-AGAA
*
210220 AAAGAAGAAAA-AAATCAGAA
1 AAA-AAGAAAAGAAA-AAGAA
210240 AAAAAGAAAAGAAAAAGAA
1 AAAAAGAAAAGAAAAAGAA
210259 A
1 A
210260 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 12 0.35
20 15 0.44
21 7 0.21
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAAGAA
Found at i:218514 original size:22 final size:23
Alignment explanation
Indices: 218482--218526 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
218472 CAACAAGTGG
*
218482 GTATCAGTACCATAGT-AGGGTA
1 GTATCAATACCATAGTAAGGGTA
*
218504 GTATCAATACCATGGTAAGGGTA
1 GTATCAATACCATAGTAAGGGTA
218527 TCGATAGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (23 bp):
GTATCAATACCATAGTAAGGGTA
Found at i:219106 original size:20 final size:20
Alignment explanation
Indices: 219033--219099 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
219023 AATTGAAAAT
219033 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
219053 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
219073 TCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
219093 GCATGAA
1 GCATGAA
219100 CAGATGCCGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:222541 original size:51 final size:51
Alignment explanation
Indices: 222471--222583 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 51
222461 AGAATTATAT
** * * * *
222471 TTATTATTTTTTTAAGAATTAAGATCGATTTAAAATATTAT-TCTTAGTTTA
1 TTATTATTTTAATAAGAATTAAGATAGAATCAAAACATTATCT-TTAGTTTA
*
222522 TTATTATTTTAATAGGAATTAAGATAGAATCAAAACATTATCTTTAGTTTA
1 TTATTATTTTAATAAGAATTAAGATAGAATCAAAACATTATCTTTAGTTTA
222573 TTATTATTTTA
1 TTATTATTTTA
222584 TTCATTAGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 53 0.98
52 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.50
Consensus pattern (51 bp):
TTATTATTTTAATAAGAATTAAGATAGAATCAAAACATTATCTTTAGTTTA
Found at i:229700 original size:16 final size:17
Alignment explanation
Indices: 229670--229703 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
229660 TCAACACTCA
229670 CTTTCTCTAAAAATTTC
1 CTTTCTCTAAAAATTTC
*
229687 CTTT-TCTAAGAATTTC
1 CTTTCTCTAAAAATTTC
229703 C
1 C
229704 ATCTTCTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (17 bp):
CTTTCTCTAAAAATTTC
Found at i:232154 original size:22 final size:24
Alignment explanation
Indices: 232120--232167 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
232110 TTAATTTCTG
232120 TTAGTGTGATATTTGTGTAAA-AT
1 TTAGTGTGATATTTGTGTAAATAT
* *
232143 TTAG-GTGTTATTTTTGTAAATAT
1 TTAGTGTGATATTTGTGTAAATAT
232166 TT
1 TT
232168 GTAGAAGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (24 bp):
TTAGTGTGATATTTGTGTAAATAT
Found at i:233590 original size:24 final size:24
Alignment explanation
Indices: 233563--233631 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
233553 CGATATGAAC
233563 TTTGATATGATACTTGACCTGGAT
1 TTTGATATGATACTTGACCTGGAT
*
233587 TTTGATATGATACTTGACCTAGAT
1 TTTGATATGATACTTGACCTGGAT
*
233611 TTTTATATGATACTTGACCTG
1 TTTGATATGATACTTGACCTG
233632 AAATATTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGATATGATACTTGACCTGGAT
Found at i:235202 original size:27 final size:23
Alignment explanation
Indices: 235128--235211 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
235118 TTTAAACTTT
* *
235128 GATCTACTCACCGTCTGACCTTC
1 GATCGACTCACCGTCCGACCTTC
235151 GATCGACTCACCGTCCGACCTTC
1 GATCGACTCACCGTCCGACCTTC
*
235174 GATCGACTCACCGTCCGACCTTT
1 GATCGACTCACCGTCCGACCTTC
235197 GATCGACTCACCGTC
1 GATCGACTCACCGTC
235212 TGACATTCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.18, C:0.40, G:0.17, T:0.25
Consensus pattern (23 bp):
GATCGACTCACCGTCCGACCTTC
Found at i:236018 original size:17 final size:17
Alignment explanation
Indices: 235996--236028 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
235986 CTTTGATCGA
235996 AAAGTCAAATTTTATGG
1 AAAGTCAAATTTTATGG
*
236013 AAAGTCATATTTTATG
1 AAAGTCAAATTTTATG
236029 TTTTTTACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (17 bp):
AAAGTCAAATTTTATGG
Found at i:242692 original size:28 final size:28
Alignment explanation
Indices: 242660--242722 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
242650 TTTCTTTTCT
* *
242660 TTTCTTTGCTTT-TTTTTAAGTGCTGGAA
1 TTTCTTT-CTTTCTTTTGAAGTGCTGCAA
* *
242688 TTTCTTTCTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTCTTTCTTTTGAAGTGCTGCAA
242716 TTTCTTT
1 TTTCTTT
242723 TTTTTCAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.60
Consensus pattern (28 bp):
TTTCTTTCTTTCTTTTGAAGTGCTGCAA
Found at i:252192 original size:53 final size:53
Alignment explanation
Indices: 252110--252223 Score: 165
Period size: 53 Copynumber: 2.2 Consensus size: 53
252100 CTATGTGTAC
* * * *
252110 TCGGCACTATGTGTGGACCCATGGTATTCATAATGAGTTTGTGAATGATCATT
1 TCGGCACTATGTATGCACCCATGGAATTCATAATGAGTTTGTGAATGACCATT
* * *
252163 TCGGCACTATGTATGCATCTATGGAATTCATAATGAGTTTGTGAATTACCATT
1 TCGGCACTATGTATGCACCCATGGAATTCATAATGAGTTTGTGAATGACCATT
252216 TCGGCACT
1 TCGGCACT
252224 TAAGTGCAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (53 bp):
TCGGCACTATGTATGCACCCATGGAATTCATAATGAGTTTGTGAATGACCATT
Found at i:263887 original size:53 final size:53
Alignment explanation
Indices: 263783--263887 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
263773 GTGTACTTTC
* * *
263783 GGCACTATGTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTGCCATTTT
1 GGCACTATGTGTGCACACATGGAATTCATAATGAGTTTGTGAATTACCATTTT
* * * *
263836 GGCATTATGTGTGCATACATGGAATTCATAATGAGTTTGTTAATTATCATTT
1 GGCACTATGTGTGCACACATGGAATTCATAATGAGTTTGTGAATTACCATTT
263888 CGGTACTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (53 bp):
GGCACTATGTGTGCACACATGGAATTCATAATGAGTTTGTGAATTACCATTTT
Found at i:266198 original size:95 final size:94
Alignment explanation
Indices: 266039--266212 Score: 260
Period size: 95 Copynumber: 1.8 Consensus size: 94
266029 AACATGGAAC
* * *
266039 CTAATTTTGGTATCAATACCAAAAGGAGTATCGGTACCATAATATAGTAGTATCGATACCATGGT
1 CTAATTTTGGTATCAATACCAAAAGGAGTATCGATACCATAACAGAGTAGTATCGATACCATGGT
266104 AAGGGTATCGATACCAGACCGTATCGAAT
66 AAGGGTATCGATACCAGACCGTATCGAAT
* * *
266133 CTAATTTTGGTATCGATACCGAAAGAGG-GTATCGATACCATAGCAGGGTAGTATCGATACCATG
1 CTAATTTTGGTATCAATACC-AAA-AGGAGTATCGATACCATAACAGAGTAGTATCGATACCATG
*
266197 GTAGGGGTATCGATAC
64 GTAAGGGTATCGATAC
266213 TGAAGAACCA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
94 19 0.27
95 49 0.69
96 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (94 bp):
CTAATTTTGGTATCAATACCAAAAGGAGTATCGATACCATAACAGAGTAGTATCGATACCATGGT
AAGGGTATCGATACCAGACCGTATCGAAT
Found at i:266208 original size:20 final size:20
Alignment explanation
Indices: 266141--266212 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 20
266131 ATCTAATTTT
*
266141 GGTATCGATACCGAAAG-A-G
1 GGTATCGATACC-ATAGCAGG
266160 GGTATCGATACCATAGCAGG
1 GGTATCGATACCATAGCAGG
* *
266180 GTAGTATCGATACCATGGTAGG
1 G--GTATCGATACCATAGCAGG
266202 GGTATCGATAC
1 GGTATCGATAC
266213 TGAAGAACCA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 3 0.07
19 13 0.28
20 12 0.26
22 18 0.39
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (20 bp):
GGTATCGATACCATAGCAGG
Found at i:266624 original size:59 final size:59
Alignment explanation
Indices: 266546--267067 Score: 737
Period size: 59 Copynumber: 8.8 Consensus size: 59
266536 CCACTAAGTA
* *
266546 TGCTAAAATGATAAGAAATTCATACTAAGCGTATGAATTTCCGTATAGGGCACTTCGTG
1 TGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTG
* * * *
266605 TGGTGAAATCG-TAAGAAATTCATACTAAGTGTATGAATTTCCATATAAGGCACTTCGTG
1 TGCTAAAAT-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTG
* * *
266664 TGCTAAAATGGTAAGAAATTCATACTAAGTAGTGTATGAATTTCCGTATAGGGAACTTAGTG
1 TGCTAAAATGTTAAGAAATTCATACT-A--AGTGTATGAATTTCCGTATAGGGCACTTCGTG
* * * *
266726 TTCTAAAATGTTAAGAAATTCATATTAAGTGTATGAGTTTCAGTATAGGGCACTTCGTG
1 TGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTG
*
266785 TGCTAAAATGTTAAGAAATTCATAATAAGTGTATGAATTTCCGTATAGGGCACTTCGTG
1 TGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTG
* *
266844 TGCTAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGAGCACTTCGTG
1 TGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTG
* *
266903 TGCTAAAATGGTAAGAAATTCATACTAAGTGTATGAATTT-CGTATAGAGCACTTCGTG
1 TGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTG
* * * *
266961 TGCTAAAATGTTAAAGAAATTCATTCTAAGTGTATGACTTTTCGTATTGGGCACCTT-GTG
1 TGCTAAAATGTT-AAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCA-CTTCGTG
* *
267021 TGCTAAAATGATATA-AAATTCATACTAAGTGTATGAATTTTCGTATA
1 TGCTAAAATGTTA-AGAAATTCATACTAAGTGTATGAATTTCCGTATA
267068 AGAAATATAG
Statistics
Matches: 420, Mismatches: 34, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
58 30 0.07
59 309 0.74
60 26 0.06
61 4 0.01
62 51 0.12
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (59 bp):
TGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTG
Found at i:268722 original size:55 final size:55
Alignment explanation
Indices: 268552--269908 Score: 1493
Period size: 55 Copynumber: 24.6 Consensus size: 55
268542 CAATAAAAAA
* * *
268552 AGGGAGCGAACCCGTTGGCAAATCAAGATTGTTCGAGTTCTACACTCCGTGAAGCAAG
1 AGGGAGCGAACCCGTTGGC--A-GAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* *
268610 AGGGAGAGAACCCGTTGGCAGAAGATGGTT-GAGTT-TCATACTCCCTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCT-ATACTCCCTGAAGCAAG
** *
268664 AGGGAATGAACCTGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * * * *
268719 AGGGAGCGAACTCATTGACAAAAGATTGTTCGAAGTTCCATACTCCCTGAAGGAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCG-AGTTCTATACTCCCTGAAGCAAG
* * *
268775 AGGGAGCGAACCCATTGACAGAAGATTGTTCGAGTT-TCATACTCCCTAAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCT-ATACTCCCTGAAGCAAG
* * * *
268830 AAGGAACGAACCCATTGGCAGAAGA-TGTTCGAGTT-TCATACTCCCTTAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCT-ATACTCCCTGAAGCAAG
* * * *
268884 AGGGAACAAACCCATTGGCAGAAGATTGTTTGAGTTCTATACTCCCTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * *
268939 AGGGAGTGAACTCGTTGACAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * *
268994 AGAGAGC-AACCCCGTTGGCAAATCAAGATTGTTCGAGTTCTATACTCTCTGAAGCAAG
1 AGGGAGCGAA-CCCGTTGGC--A-GAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * *
269052 AGGGAGCGAACCCATTGGCAGAAGA-TGTTCGGGTT-TCATACTCCCTGAAGAAAA
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCT-ATACTCCCTGAAGCAAG
** ** * *
269106 AGGGAATGAACCTATTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGTAGAAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
** * * * *
269161 AGGGAGCGAACTTGTTGACAGAAGATTGTTCGAGTTCCATATTCTCTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * * *
269216 AGGGAGTGAACCCATTGGCAAATCAAGATTGTTCGAGTTCCATACTCCCTGAAGTAAG
1 AGGGAGCGAACCCGTTGGC--A-GAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * * *
269274 AGGGAGCAAACCCGTTGGTAGAAGATTGTTCGAGTTCCATACTCCGTAAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * *
269329 AGGGAGCAAACTCGTTGACAGAAGATTATTCGAGTTCTATACTCCCTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * * *
269384 AGGGAGTGAACTCGTTGACAGAAGATTGTTCGAGTTCCATACTCCCTGAAGTAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * *
269439 AGGGAGTGAACCCGTTGGCAAATCAAGATTGTTCAAGTTAC-AAACTCCCTGAAGCAAG
1 AGGGAGCGAACCCGTTGGC--A-GAAGATTGTTCGAGTT-CTATACTCCCTGAAGCAAG
* * * * **
269497 AGGGAGCAAACTCGTTGGCAGAAGATTGTTTGAGTTCCATACTCTTTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * *
269552 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATTCTGCCTTAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * *
269607 AGGGAGCAAACCTGTTGACAGAAGATTTGTTCGAGTTCCATACTCCCTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGA-TTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * *
269663 AGGGAGCGAACCCATTGGCAGAATATTGTTCGAGTTCTATACTCCATGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * * * * * *
269718 AGGGAACGAACCCATTGGTAAAAGATTGTTAGAGTTCTACACTCCCTGATGTAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* * * *
269773 AGGGAACGAACCCATAGGCAGAAGATTGTTCGAGTTC--TACTCCTTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* *
269826 AGGGAGCGAACCCATAGGCAGAAGATTGTTCGAGTTC--TACTCCCTGAAGCAAG
1 AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
* *
269879 ATGGAG-GAACCCGCTGGTC-GAAGATTGTTC
1 AGGGAGCGAACCCGTTGG-CAGAAGATTGTTC
269909 AAAGAAGAGT
Statistics
Matches: 1115, Mismatches: 159, Indels: 56
0.84 0.12 0.04
Matches are distributed among these distances:
52 19 0.02
53 71 0.06
54 145 0.13
55 615 0.55
56 104 0.09
57 3 0.00
58 155 0.14
59 3 0.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (55 bp):
AGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
Found at i:269334 original size:168 final size:166
Alignment explanation
Indices: 268552--269890 Score: 1520
Period size: 168 Copynumber: 8.1 Consensus size: 166
268542 CAATAAAAAA
* * * * * *
268552 AGGGAGCGAACCCGTTGGCAAATCAAGATTGTTCGAGTTCTACACTCCGTGAAGCAAGAGGGAGA
1 AGGGAGCGAACCCATTGGC-AA-GAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGC
* * ** *
268617 GAACCCGTTGGCAGAAGATGGTT-GAGTTTCATACTCCCTGAAGCAAGAGGGAATGAACCTGTTG
64 GAACCCGTTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTG
*
268681 GCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAG
129 GCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
* * *
268719 AGGGAGCGAACTCATTGACAA-AAGATTGTTCGAAGTTCCATACTCCCTGAAGGAAGAGGGAGCG
1 AGGGAGCGAACCCATTGGCAAGAAGATTGTTCG-AGTTCCATACTCCCTGAAGCAAGAGGGAGCG
* * * * * * *
268783 AACCCATTGACAGAAGATTGTTCGAGTTTCATACTCCCTAAAGCAAGAAGGAACGAACCCATTGG
65 AACCCGTTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGG
* *
268848 CAGAAGA-TGTTCGAGTTTCATACTCCCTTAAGCAAG
130 CAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
* * * * *
268884 AGGGAACAAACCCATTGGC-AGAAGATTGTTTGAGTTCTATACTCCCTGAAGCAAGAGGGAGTGA
1 AGGGAGCGAACCCATTGGCAAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGA
* * *
268948 ACTCGTTGACAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGAGAGC-AACCCCGTTGG
66 ACCCGTTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAA-CCCGTTGG
* * *
269012 CAAATCAAGATTGTTCGAGTTCTATACTCTCTGAAGCAAG
130 C--A-GAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
* * * * **
269052 AGGGAGCGAACCCATTGGC-AGAAGA-TGTTCGGGTTTCATACTCCCTGAAGAAAAAGGGAATGA
1 AGGGAGCGAACCCATTGGCAAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGA
** * * * ** *
269115 ACCTATTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGTAGAAAGAGGGAGCGAACTTGTTGAC
66 ACCCGTTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
* *
269180 AGAAGATTGTTCGAGTTCCATATTCTCTGAAGCAAG
131 AGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
* * *
269216 AGGGAGTGAACCCATTGGCAAATCAAGATTGTTCGAGTTCCATACTCCCTGAAGTAAGAGGGAGC
1 AGGGAGCGAACCCATTGGC-AA-GAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGC
* * * * * *
269281 AAACCCGTTGGTAGAAGATTGTTCGAGTTCCATACTCCGTAAAGCAAGAGGGAGCAAACTCGTTG
64 GAACCCGTTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTG
* * *
269346 ACAGAAGATTATTCGAGTTCTATACTCCCTGAAGCAAG
129 GCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
* * * * * *
269384 AGGGAGTGAACTCGTTGAC-AGAAGATTGTTCGAGTTCCATACTCCCTGAAGTAAGAGGGAGTGA
1 AGGGAGCGAACCCATTGGCAAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGA
* * * * * *
269448 ACCCGTTGGCAAATCAAGATTGTTCAAGTTACAAACTCCCTGAAGCAAGAGGGAGCAAACTCGTT
66 ACCCGTTGGC--A-GAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAACCCGTT
* **
269513 GGCAGAAGATTGTTTGAGTTCCATACTCTTTGAAGCAAG
128 GGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
* * * * * *
269552 AGGGAGCGAACCCGTTGGC-AGAAGATTGTTCGAGTTCTATTCTGCCTTAAGCAAGAGGGAGCAA
1 AGGGAGCGAACCCATTGGCAAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGA
* * *
269616 ACCTGTTGACAGAAGATTTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAACCCATTGG
66 ACCCGTTGGCAGAAGA-TTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGG
* * *
269681 CAGAATATTGTTCGAGTTCTATACTCCATGAAGCAAG
130 CAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
* * * * * * * *
269718 AGGGAACGAACCCATTGGTAA-AAGATTGTTAGAGTTCTACACTCCCTGATGTAAGAGGGAACGA
1 AGGGAGCGAACCCATTGGCAAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGA
* * * * *
269782 ACCCATAGGCAGAAGATTGTTCGAGTT-C-TACTCCTTGAAGCAAGAGGGAGCGAACCCATAGGC
66 ACCCGTTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
269845 AGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAG
131 AGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
*
269879 ATGGAG-GAACCC
1 AGGGAGCGAACCC
269891 GCTGGTCGAA
Statistics
Matches: 1002, Mismatches: 152, Indels: 43
0.84 0.13 0.04
Matches are distributed among these distances:
160 6 0.01
161 19 0.02
163 51 0.05
164 146 0.15
165 162 0.16
166 186 0.19
167 108 0.11
168 324 0.32
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (166 bp):
AGGGAGCGAACCCATTGGCAAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGA
ACCCGTTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
AGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAG
Found at i:269423 original size:223 final size:223
Alignment explanation
Indices: 268552--269890 Score: 1661
Period size: 223 Copynumber: 6.1 Consensus size: 223
268542 CAATAAAAAA
* * * *
268552 AGGGAGCGAACCCGTTGGCAAATCAAGATTGTTCGAGTTCTACACTCCGTGAAGCAAGAGGGAG-
1 AGGGAGCGAACCCATTGGCAAATCAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGC
* * * *** **
268616 AGAACCCGTTGGCAGAAGATGGTT-GAGTTTCATACTCCCTGAAGCAAGAGGGAATGAACCTGTT
66 A-AACCCATTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCAAACCCATT
* *
268680 GGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACTCATTGACAAAAGAT
130 GGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACTCGTTGACAGAAGAT
*
268745 TGTTCGAAGTTCCATACTCCCTGAAGGAAG
195 TGTTCG-AGTTCCATACTCCCTGAAGCAAG
* * * * * *
268775 AGGGAGCGAACCCATT-G-ACA-GAAGATTGTTCGAGTTTCATACTCCCTAAAGCAAGAAGGAAC
1 AGGGAGCGAACCCATTGGCAAATCAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGC
* * * *
268837 GAACCCATTGGCAGAAGA-TGTTCGAGTTTCATACTCCCTTAAGCAAGAGGGAACAAACCCATTG
66 AAACCCATTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCAAACCCATTG
* *
268901 GCAGAAGATTGTTTGAGTTCTATACTCCCTGAAGCAAGAGGGAGTGAACTCGTTGACAGAAGATT
131 GCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACTCGTTGACAGAAGATT
268966 GTTCGAGTTCCATACTCCCTGAAGCAAG
196 GTTCGAGTTCCATACTCCCTGAAGCAAG
* * * *
268994 AGAGAGC-AACCCCGTTGGCAAATCAAGATTGTTCGAGTTCTATACTCTCTGAAGCAAGAGGGAG
1 AGGGAGCGAA-CCCATTGGCAAATCAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAG
* * * * * *** *
269058 CGAACCCATTGGCAGAAGA-TGTTCGGGTTTCATACTCCCTGAAGAAAAAGGGAATGAACCTATT
65 CAAACCCATTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCAAACCCATT
* * *
269122 GGCAGAAGATTGTTCGAGTTCTATACTCCCTGTAGAAAGAGGGAGCGAACTTGTTGACAGAAGAT
130 GGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACTCGTTGACAGAAGAT
* *
269187 TGTTCGAGTTCCATATTCTCTGAAGCAAG
195 TGTTCGAGTTCCATACTCCCTGAAGCAAG
* *
269216 AGGGAGTGAACCCATTGGCAAATCAAGATTGTTCGAGTTCCATACTCCCTGAAGTAAGAGGGAGC
1 AGGGAGCGAACCCATTGGCAAATCAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGC
* * * * * *
269281 AAACCCGTTGGTAGAAGATTGTTCGAGTTCCATACTCCGTAAAGCAAGAGGGAGCAAACTCGTTG
66 AAACCCATTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCAAACCCATTG
* * *
269346 ACAGAAGATTATTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGTGAACTCGTTGACAGAAGATT
131 GCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACTCGTTGACAGAAGATT
*
269411 GTTCGAGTTCCATACTCCCTGAAGTAAG
196 GTTCGAGTTCCATACTCCCTGAAGCAAG
* * * * *
269439 AGGGAGTGAACCCGTTGGCAAATCAAGATTGTTCAAGTTACAAACTCCCTGAAGCAAGAGGGAGC
1 AGGGAGCGAACCCATTGGCAAATCAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGC
* * * ** * *
269504 AAACTCGTTGGCAGAAGATTGTTTGAGTTCCATACTCTTTGAAGCAAGAGGGAGCGAACCCGTTG
66 AAACCCATTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCAAACCCATTG
* * * *
269569 GCAGAAGATTGTTCGAGTTCTATTCTGCCTTAAGCAAGAGGGAGCAAAC-CTGTTGACAGAAGAT
131 GCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACTC-GTTGACAGAAGA-
269633 TTGTTCGAGTTCCATACTCCCTGAAGCAAG
194 TTGTTCGAGTTCCATACTCCCTGAAGCAAG
* * *
269663 AGGGAGCGAACCCATTGGCAGAAT----ATTGTTCGAGTTCTATACTCCATGAAGCAAGAGGGAA
1 AGGGAGCGAACCCATTGGCA-AATCAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAG
* * * * * * * * * * *
269724 CGAACCCATTGGTAAAAGATTGTTAGAGTTCTACACTCCCTGATGTAAGAGGGAACGAACCCATA
65 CAAACCCATTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCAAACCCATT
* * * * *
269789 GGCAGAAGATTGTTCGAGTTC--TACTCCTTGAAGCAAGAGGGAGCGAACCCATAGGCAGAAGAT
130 GGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACTCGTTGACAGAAGAT
269852 TGTTCGAGTT-C-TACTCCCTGAAGCAAG
195 TGTTCGAGTTCCATACTCCCTGAAGCAAG
*
269879 ATGGAG-GAACCC
1 AGGGAGCGAACCC
269891 GCTGGTCGAA
Statistics
Matches: 974, Mismatches: 130, Indels: 32
0.86 0.11 0.03
Matches are distributed among these distances:
215 6 0.01
216 21 0.02
217 1 0.00
218 13 0.01
219 67 0.07
220 153 0.16
221 106 0.11
222 251 0.26
223 306 0.31
224 47 0.05
225 3 0.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (223 bp):
AGGGAGCGAACCCATTGGCAAATCAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGC
AAACCCATTGGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAAGAGGGAGCAAACCCATTG
GCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACTCGTTGACAGAAGATT
GTTCGAGTTCCATACTCCCTGAAGCAAG
Done.