Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008413.1 Hibiscus syriacus cultivar Beakdansim tig00111191_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: 2772818
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:2579493 original size:19 final size:19
Alignment explanation
Indices: 2579471--2579534 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
2579461 GAAATGAAAA
2579471 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2579490 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2579506 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2579523 TCGCATTGCGAT
1 TCGCATTGCGAT
2579535 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 17 0.46
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2579553 original size:20 final size:19
Alignment explanation
Indices: 2579519--2579572 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
2579509 TTGCGATTTT
*
2579519 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2579538 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2579558 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
2579573 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2579571 original size:19 final size:19
Alignment explanation
Indices: 2579507--2579572 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
2579497 GCGATTTTGT
**
2579507 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
2579526 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
2579546 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
2579565 TGTTGCGA
1 CGTTGCGA
2579573 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:2580071 original size:18 final size:18
Alignment explanation
Indices: 2580045--2580089 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2580035 GTCGATCAGA
* *
2580045 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
2580063 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2580081 TGATGGCTC
1 TGATGGCTC
2580090 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2581649 original size:22 final size:22
Alignment explanation
Indices: 2581624--2581667 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2581614 GATTTAGATA
2581624 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2581646 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2581668 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2581948 original size:20 final size:20
Alignment explanation
Indices: 2581835--2581948 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
2581825 CGCTTTGAAA
2581835 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
2581855 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
2581875 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
2581895 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
2581916 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
2581936 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2581949 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 56 0.73
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:2581967 original size:41 final size:41
Alignment explanation
Indices: 2581878--2582010 Score: 128
Period size: 41 Copynumber: 3.2 Consensus size: 41
2581868 AGTCAGTATC
* * * **
2581878 GCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT--GTATTAT
1 GCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATT-T
*
2581918 CGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATTT
1 -GCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATTT
* ** *
2581960 GCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAATTC
1 GCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAATTT
2582001 GCGTTGCGAT
1 GCGTTGCGAT
2582011 TTACTTATTC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 70 0.90
42 1 0.01
43 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
GCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAATTT
Found at i:2581968 original size:21 final size:21
Alignment explanation
Indices: 2581937--2582012 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2581927 ATAGTAAGTA
*
2581937 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
2581958 TTGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
2581978 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
2581999 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
2582013 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:2581988 original size:20 final size:20
Alignment explanation
Indices: 2581963--2582029 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
2581953 CCAATTTGCG
2581963 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
2581983 TTGCGATTTTCCCAATTCGCG
1 TTGCGA-TTTACTTATTCGCA
2582004 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
2582024 TTGCGA
1 TTGCGA
2582030 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:2582011 original size:41 final size:41
Alignment explanation
Indices: 2581937--2582029 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
2581927 ATAGTAAGTA
*
2581937 TCGCATTGCGATTTTCCCAATTTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
2581978 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
2582019 TCGCATTGCGA
1 TCGCATTGCGA
2582030 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2586324 original size:18 final size:19
Alignment explanation
Indices: 2586283--2586324 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
2586273 ATTTCAACCT
2586283 TTTTTATCTTTTCTTCTAA
1 TTTTTATCTTTTCTTCTAA
2586302 TTTTT-TCTTCTTCTTC-AA
1 TTTTTATCTT-TTCTTCTAA
2586320 TTTTT
1 TTTTT
2586325 CAAGCAGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTATCTTTTCTTCTAA
Found at i:2598505 original size:12 final size:12
Alignment explanation
Indices: 2598488--2598512 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2598478 CGCGTTACAT
2598488 TTATCATTATTG
1 TTATCATTATTG
2598500 TTATCATTATTG
1 TTATCATTATTG
2598512 T
1 T
2598513 AGACTGTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTATCATTATTG
Found at i:2599780 original size:2 final size:2
Alignment explanation
Indices: 2599773--2599799 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2599763 TGGTTTAGCT
2599773 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2599800 GTGTGTGATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2603267 original size:34 final size:34
Alignment explanation
Indices: 2603229--2603306 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
2603219 GATGAATGCA
2603229 GTGAAGGAGAAGGAAG-AAGAGTAAAGAATGAGTT
1 GTGAAGGAGAA-GAAGAAAGAGTAAAGAATGAGTT
* * *
2603263 GTGAAGAAGGAGAAGAAAGAGTGAAGAATGAGTT
1 GTGAAGGAGAAGAAGAAAGAGTAAAGAATGAGTT
*
2603297 GGGAAGGAGA
1 GTGAAGGAGA
2603307 TTCCTAACGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 4 0.11
34 33 0.89
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.13
Consensus pattern (34 bp):
GTGAAGGAGAAGAAGAAAGAGTAAAGAATGAGTT
Found at i:2603497 original size:20 final size:20
Alignment explanation
Indices: 2603451--2603498 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2603441 TTAGTCAAAG
*
2603451 GGTCATGGAAGCAGTTAACT
1 GGTCATGTAAGCAGTTAACT
*
2603471 GGTCATGTAAGCATTTAAC-
1 GGTCATGTAAGCAGTTAACT
2603490 GGTACATGT
1 GGT-CATGT
2603499 CAATTTTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (20 bp):
GGTCATGTAAGCAGTTAACT
Found at i:2605483 original size:60 final size:60
Alignment explanation
Indices: 2605410--2605547 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
2605400 ATTTTAAATG
* * *
2605410 TTTCAATTTCATCCCTAAACTATGAC-TATCGTTCTAAATTAGTCCTCAAACT-TTTGAACA
1 TTTCAATTCCATCCC-AAACTATGACGT-TCATTCTAAATTAGTCCCCAAACTATTTGAACA
* * *
2605470 TTTCAATTCCATCCCCAACTATGACGTTCATTCTAAATTGGTCCCCAAACTATTTGAGCA
1 TTTCAATTCCATCCCAAACTATGACGTTCATTCTAAATTAGTCCCCAAACTATTTGAACA
* *
2605530 TTCCAATTCAATCCCAAA
1 TTTCAATTCCATCCCAAA
2605548 TTATACATAT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 30 0.45
60 37 0.55
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (60 bp):
TTTCAATTCCATCCCAAACTATGACGTTCATTCTAAATTAGTCCCCAAACTATTTGAACA
Found at i:2605546 original size:59 final size:59
Alignment explanation
Indices: 2605427--2605544 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 59
2605417 TTCATCCCTA
* * * *
2605427 AACTATGACTATCGTTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTCCATCCCC
1 AACTATGACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTCCAATTCAATCCCC
* *
2605486 AACTATGACGT-TCATTCTAAATTGGTCCCCAAACTATTTGAGCATTCCAATTCAATCCC
1 AACTATGAC-TATCATTCTAAATTAGTCCCCAAACT-TTTGAACATTCCAATTCAATCCC
2605545 AAATTATACA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 30 0.59
60 21 0.41
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (59 bp):
AACTATGACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTCCAATTCAATCCCC
Found at i:2605819 original size:58 final size:59
Alignment explanation
Indices: 2605704--2605819 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 59
2605694 AGTTTGGGGA
* *** *
2605704 ACTAATTTAGAAAGATGGTCATAGTTTAGGGATGAAATTAGAATGTTTGAAAGTTTAATG
1 ACTAATTTAGAAAGA-GGTCATAGTTTAGGGATGAAATTAGAATATCCCAAAATTTAATG
* *
2605764 ACTAATTTAGAATGA-GTCATAGTTTTGGGGATGAAATTA-AATATCCCAAAATTTAA
1 ACTAATTTAGAAAGAGGTCATAG-TTTAGGGATGAAATTAGAATATCCCAAAATTTAA
2605820 GGACCGATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 19 0.40
59 15 0.31
60 14 0.29
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (59 bp):
ACTAATTTAGAAAGAGGTCATAGTTTAGGGATGAAATTAGAATATCCCAAAATTTAATG
Found at i:2615482 original size:60 final size:60
Alignment explanation
Indices: 2615345--2615492 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 60
2615335 AACATGATAA
* * * * *
2615345 ATAGTCGG-GTAACCATTTTGTAACCTTTAATAGTCTAAGAACTCAATGAAGTAATACTTT
1 ATAGTCGGAG-AACCATTTTGTAACTTTTAATAATCGAAGAACTCAATAAAGTAATACCTT
* * * *
2615405 ATAATCGAATG-ATCATTTTGTAACTTTTAATAATCGAGAGAA-TCGATAAAGTAATACCTT
1 ATAGTCGGA-GAACCATTTTGTAACTTTTAATAATCGA-AGAACTCAATAAAGTAATACCTT
2615465 ATAGTCGGAGAACCATTTGTGT-ACTTTT
1 ATAGTCGGAGAACCATTT-TGTAACTTTT
2615493 CCAAAAAATT
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
59 1 0.01
60 62 0.87
61 7 0.10
62 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (60 bp):
ATAGTCGGAGAACCATTTTGTAACTTTTAATAATCGAAGAACTCAATAAAGTAATACCTT
Found at i:2615801 original size:26 final size:27
Alignment explanation
Indices: 2615772--2615822 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2615762 ATAAATTTAA
*
2615772 TAATTATTTTAAA-AATT-TTAAAATTT
1 TAATTA-TTAAAATAATTATTAAAATTT
2615798 TAATTATTAAAATAATTATTAAAAT
1 TAATTATTAAAATAATTATTAAAAT
2615823 ATAATTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 10 0.45
27 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TAATTATTAAAATAATTATTAAAATTT
Found at i:2615815 original size:12 final size:12
Alignment explanation
Indices: 2615798--2615823 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2615788 TTTAAAATTT
2615798 TAATTATTAAAA
1 TAATTATTAAAA
2615810 TAATTATTAAAA
1 TAATTATTAAAA
2615822 TA
1 TA
2615824 TAATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATTATTAAAA
Found at i:2615827 original size:26 final size:26
Alignment explanation
Indices: 2615771--2615828 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
2615761 AATAAATTTA
*
2615771 ATAATTATTTTAAAAATTTTAAAATT
1 ATAATTATTTAAAAAATTTTAAAATT
*
2615797 TTAATTA-TTAAAATAATTATTAAAA-T
1 ATAATTATTTAAAA-AATT-TTAAAATT
2615823 ATAATT
1 ATAATT
2615829 TAATTTATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
26 16 0.59
27 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATAATTATTTAAAAAATTTTAAAATT
Found at i:2616440 original size:16 final size:16
Alignment explanation
Indices: 2616419--2616457 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2616409 ATTATTTTAT
2616419 TATGTTTCTTAATGGA
1 TATGTTTCTTAATGGA
2616435 TATGTTTCTTAATGGA
1 TATGTTTCTTAATGGA
*
2616451 AATGTTT
1 TATGTTT
2616458 TTTTTATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (16 bp):
TATGTTTCTTAATGGA
Found at i:2619883 original size:15 final size:15
Alignment explanation
Indices: 2619865--2619920 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2619855 TAACCGGTTT
2619865 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2619880 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
2619897 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2619912 CGATTTTAA
1 CGGTTTTAA
2619921 TATTCCAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:2619893 original size:17 final size:17
Alignment explanation
Indices: 2619868--2619918 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2619858 CCGGTTTCGG
2619868 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
2619885 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
2619900 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
2619917 TT
1 TT
2619919 AATATTCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:2620338 original size:13 final size:13
Alignment explanation
Indices: 2620317--2620371 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2620307 AAGTTCGATA
*
2620317 AATTCAAATACTT
1 AATTGAAATACTT
2620330 AATTGAAATACTT
1 AATTGAAATACTT
* *
2620343 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
2620357 AATTGAAATACTT
1 AATTGAAATACTT
2620370 AA
1 AA
2620372 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:2620453 original size:32 final size:33
Alignment explanation
Indices: 2620357--2620455 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2620347 AACTCAACAT
* * *
2620357 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2620390 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2620423 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2620455 A
1 A
2620456 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:2620474 original size:21 final size:21
Alignment explanation
Indices: 2620450--2620489 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2620440 ACTTCAAGTT
2620450 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2620471 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
2620490 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2623489 original size:21 final size:21
Alignment explanation
Indices: 2623463--2623507 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2623453 GATTTCTGGG
* *
2623463 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2623484 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2623505 CAA
1 CAA
2623508 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2624456 original size:2 final size:2
Alignment explanation
Indices: 2624449--2624490 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2624439 GAACATGTGA
2624449 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
2624491 CTAAGAGAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2625074 original size:32 final size:32
Alignment explanation
Indices: 2625033--2625129 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
2625023 GAGTCGATGG
2625033 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
2625065 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
2625096 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
2625128 TT
1 TT
2625130 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:2625105 original size:31 final size:31
Alignment explanation
Indices: 2625032--2625132 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
2625022 AGAGTCGATG
2625032 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
2625063 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
2625095 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
2625126 GTTTACC
1 GTTTACC
2625133 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:2625164 original size:30 final size:30
Alignment explanation
Indices: 2625128--2625187 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2625118 TATGGACAGT
2625128 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
2625158 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
2625188 GTCTTTCGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:2627864 original size:32 final size:32
Alignment explanation
Indices: 2627823--2627919 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
2627813 GAGTCGATGG
2627823 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
2627855 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
2627886 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
2627918 TT
1 TT
2627920 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:2627895 original size:31 final size:31
Alignment explanation
Indices: 2627822--2627922 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
2627812 AGAGTCGATG
2627822 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
2627853 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
2627885 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
2627916 GTTTACC
1 GTTTACC
2627923 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:2627954 original size:30 final size:30
Alignment explanation
Indices: 2627918--2627977 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2627908 TATGGACAGT
2627918 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
2627948 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
2627978 GTCTTTCGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:2631263 original size:21 final size:21
Alignment explanation
Indices: 2631237--2631281 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2631227 GATTTCTGGG
* *
2631237 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2631258 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2631279 CAA
1 CAA
2631282 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2632230 original size:2 final size:2
Alignment explanation
Indices: 2632223--2632248 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2632213 GAACATGTGA
2632223 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
2632249 CTAAGAGAAG
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):
AT
Found at i:2632846 original size:32 final size:32
Alignment explanation
Indices: 2632791--2632887 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
2632781 GAGTCGAGGG
*
2632791 TTTACCTATATTCT-ACGGAACATATGGACAGT
1 TTTACCTATGTTCTAAC-GAACATATGGACAGT
**
2632823 TTTACCTATG-TCTTTCGAGACATATGGACAG-
1 TTTACCTATGTTCTAACGA-ACATATGGACAGT
* *
2632854 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTAACGAACATATGGACAGT
2632886 TT
1 TT
2632888 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTAACGAACATATGGACAGT
Found at i:2632863 original size:31 final size:31
Alignment explanation
Indices: 2632790--2632890 Score: 116
Period size: 31 Copynumber: 3.2 Consensus size: 31
2632780 AGAGTCGAGG
*
2632790 GTTTACCTATATTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
2632821 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
2632853 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
2632884 GTTTACC
1 GTTTACC
2632891 GAGGATCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
31 32 0.54
32 27 0.46
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:2632922 original size:30 final size:30
Alignment explanation
Indices: 2632886--2632974 Score: 178
Period size: 30 Copynumber: 3.0 Consensus size: 30
2632876 TATGGACAGT
2632886 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
2632916 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
2632946 TTACCGAGGATCTTTATGACCTCTGGATA
1 TTACCGAGGATCTTTATGACCTCTGGATA
2632975 AGTCTTTCGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:2635429 original size:21 final size:21
Alignment explanation
Indices: 2635390--2635429 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2635380 TTACAGTAAC
*
2635390 GACGTAATAGTTCACGGTGCT
1 GACGTAATAGTCCACGGTGCT
* *
2635411 GACGTGATAGTCCATGGTG
1 GACGTAATAGTCCACGGTG
2635430 TTGATGTGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.28
Consensus pattern (21 bp):
GACGTAATAGTCCACGGTGCT
Found at i:2641741 original size:20 final size:20
Alignment explanation
Indices: 2641698--2641735 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2641688 TGACTTCCGC
2641698 TATACCTTAACACTTTTCGA
1 TATACCTTAACACTTTTCGA
*
2641718 TATACCTTATCACTTTTC
1 TATACCTTAACACTTTTC
2641736 TTTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (20 bp):
TATACCTTAACACTTTTCGA
Found at i:2643880 original size:2 final size:2
Alignment explanation
Indices: 2643873--2643910 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2643863 TCGTAACTAG
2643873 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
2643911 GCACATAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2648535 original size:14 final size:14
Alignment explanation
Indices: 2648516--2648549 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
2648506 CATTCGATTA
2648516 TATGTTCGTTCATT
1 TATGTTCGTTCATT
2648530 TATGTTCGTTCATT
1 TATGTTCGTTCATT
2648544 TATGTT
1 TATGTT
2648550 AATTTATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.59
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:2648868 original size:10 final size:10
Alignment explanation
Indices: 2648853--2648892 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2648843 TATTATGTTC
*
2648853 GTTCGTTTGT
1 GTTCGTTTAT
*
2648863 GTTCGTTTAC
1 GTTCGTTTAT
*
2648873 ATTCGTTTAT
1 GTTCGTTTAT
2648883 GTTCGTTTAT
1 GTTCGTTTAT
2648893 CATTTAAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:2648879 original size:20 final size:21
Alignment explanation
Indices: 2648854--2648896 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
2648844 ATTATGTTCG
*
2648854 TTCGTTTGTGTTCGTTTA-CA
1 TTCGTTTATGTTCGTTTATCA
2648874 TTCGTTTATGTTCGTTTATCA
1 TTCGTTTATGTTCGTTTATCA
2648895 TT
1 TT
2648897 TAAATGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.58
Consensus pattern (21 bp):
TTCGTTTATGTTCGTTTATCA
Found at i:2655670 original size:14 final size:15
Alignment explanation
Indices: 2655642--2655671 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2655632 CACAATTCTT
2655642 TATGTTTTTTATGAC
1 TATGTTTTTTATGAC
2655657 TATGTTTTTT-TGAC
1 TATGTTTTTTATGAC
2655671 T
1 T
2655672 CATAAAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.17, C:0.07, G:0.13, T:0.63
Consensus pattern (15 bp):
TATGTTTTTTATGAC
Found at i:2657963 original size:27 final size:27
Alignment explanation
Indices: 2657930--2658162 Score: 295
Period size: 27 Copynumber: 8.4 Consensus size: 27
2657920 CAGCTGGAAT
2657930 GCCACCCAACAACATGGGAGGGATGCC
1 GCCACCCAACAACATGGGAGGGATGCC
*
2657957 GCCACCCAACAACAACATGGGAGGTATGCC
1 GCCA-CC--CAACAACATGGGAGGGATGCC
* *
2657987 GCCACCAAACAACATGGGAGGTATGCC
1 GCCACCCAACAACATGGGAGGGATGCC
* *
2658014 GCCACCAAACAACATGGGAGGTATGCC
1 GCCACCCAACAACATGGGAGGGATGCC
*
2658041 GCCACCAAACAACAACATGGGAGGTATGCC
1 GCCACC---CAACAACATGGGAGGGATGCC
* * * *
2658071 ACCACCAAACAATATGAGAGGGATGCC
1 GCCACCCAACAACATGGGAGGGATGCC
* *
2658098 ACCACCCAACAACATGGGAGGGATGTC
1 GCCACCCAACAACATGGGAGGGATGCC
*
2658125 GCCACCCAACAACATGGGAGGGATGTC
1 GCCACCCAACAACATGGGAGGGATGCC
2658152 GCCACCCAACA
1 GCCACCCAACA
2658163 TGGGGAATAT
Statistics
Matches: 187, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
27 134 0.72
28 2 0.01
29 2 0.01
30 49 0.26
ACGTcount: A:0.34, C:0.31, G:0.25, T:0.10
Consensus pattern (27 bp):
GCCACCCAACAACATGGGAGGGATGCC
Found at i:2658025 original size:84 final size:84
Alignment explanation
Indices: 2657930--2658162 Score: 337
Period size: 84 Copynumber: 2.8 Consensus size: 84
2657920 CAGCTGGAAT
2657930 GCCACCCAACAACATGGGAGGGATGCCGCCACCCAACAACAACATGGGAGGTATGCCGCCACCAA
1 GCCACCCAACAACATGGGAGGGATGCCGCCACCCAACAACAACATGGGAGGTATGCCGCCACCAA
* *
2657995 ACAACATGGGAGGTATGCC
66 ACAACATGAGAGGGATGCC
* * * *
2658014 GCCACCAAACAACATGGGAGGTATGCCGCCACCAAACAACAACATGGGAGGTATGCCACCACCAA
1 GCCACCCAACAACATGGGAGGGATGCCGCCACCCAACAACAACATGGGAGGTATGCCGCCACCAA
*
2658079 ACAATATGAGAGGGATGCC
66 ACAACATGAGAGGGATGCC
* * * * *
2658098 ACCACCCAACAACATGGGAGGGATGTCGCCA-CC--CAACAACATGGGAGGGATGTCGCCACCCA
1 GCCACCCAACAACATGGGAGGGATGCCGCCACCCAACAACAACATGGGAGGTATGCCGCCACCAA
2658160 ACA
66 ACA
2658163 TGGGGAATAT
Statistics
Matches: 133, Mismatches: 16, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
81 28 0.21
83 1 0.01
84 104 0.78
ACGTcount: A:0.34, C:0.31, G:0.25, T:0.10
Consensus pattern (84 bp):
GCCACCCAACAACATGGGAGGGATGCCGCCACCCAACAACAACATGGGAGGTATGCCGCCACCAA
ACAACATGAGAGGGATGCC
Found at i:2658745 original size:21 final size:23
Alignment explanation
Indices: 2658706--2658764 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
2658696 GACTCAAAAT
* *
2658706 AATAAAAATATTAT-TTTTATTC
1 AATAAAAATAATATATTTAATTC
*
2658728 AATAAAAATAATA-ATTTAATTG
1 AATAAAAATAATATATTTAATTC
2658750 AA-AAAAATAATATAT
1 AATAAAAATAATATAT
2658765 AGAGGGGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 10 0.31
22 22 0.69
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AATAAAAATAATATATTTAATTC
Found at i:2660069 original size:41 final size:41
Alignment explanation
Indices: 2660022--2660105 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
2660012 TCTCTTCATT
2660022 TCTTCTTATTCCTTTCTCCATCACTTTTTCTCCATTCTTCC
1 TCTTCTTATTCCTTTCTCCATCACTTTTTCTCCATTCTTCC
2660063 TCTTCTTATTCCTTTCTCCATCACTTTTTCTCCATTCTTCC
1 TCTTCTTATTCCTTTCTCCATCACTTTTTCTCCATTCTTCC
2660104 TC
1 TC
2660106 CTAAGCACCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.54
Consensus pattern (41 bp):
TCTTCTTATTCCTTTCTCCATCACTTTTTCTCCATTCTTCC
Found at i:2660572 original size:20 final size:20
Alignment explanation
Indices: 2660547--2660584 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2660537 AATATTATTG
*
2660547 TACTGTATGAATAGTATCAA
1 TACTGTATAAATAGTATCAA
*
2660567 TACTGTTTAAATAGTATC
1 TACTGTATAAATAGTATC
2660585 GTGAACAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (20 bp):
TACTGTATAAATAGTATCAA
Found at i:2661328 original size:15 final size:14
Alignment explanation
Indices: 2661304--2661342 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
2661294 ATCCATTTTT
2661304 CATAACATATCACA
1 CATAACATATCACA
2661318 CATACACATATCACA
1 CATA-ACATATCACA
* *
2661333 TATAATATAT
1 CATAACATAT
2661343 TTATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (14 bp):
CATAACATATCACA
Found at i:2661486 original size:23 final size:24
Alignment explanation
Indices: 2661446--2661502 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
2661436 GTATAAATTC
* * *
2661446 ACCGAAGTACCTCGTAGAATTG-T
1 ACCGAAGTGCCGCGTAGAAATGCT
*
2661469 ACCGAAGTGCCGCTTAGAAATGCT
1 ACCGAAGTGCCGCGTAGAAATGCT
2661493 -CCGAAGTGCC
1 ACCGAAGTGCC
2661503 ATATAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (24 bp):
ACCGAAGTGCCGCGTAGAAATGCT
Found at i:2667169 original size:32 final size:32
Alignment explanation
Indices: 2667096--2667172 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
2667086 TGATATTTTT
2667096 ATTTTTTTAAAAATAAAAATATTATTTTTAAA
1 ATTTTTTTAAAAATAAAAATATTATTTTTAAA
****
2667128 AAAAATTTAAAAATAAAAATATTATTTTTAAA
1 ATTTTTTTAAAAATAAAAATATTATTTTTAAA
*
2667160 TTTTTTTTAAAAA
1 ATTTTTTTAAAAA
2667173 AATAATCAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATTTTTTTAAAAATAAAAATATTATTTTTAAA
Found at i:2684586 original size:23 final size:22
Alignment explanation
Indices: 2684527--2684593 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
2684517 TATGGACATC
*
2684527 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2684549 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2684571 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
2684594 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:2687457 original size:34 final size:33
Alignment explanation
Indices: 2687419--2687492 Score: 76
Period size: 34 Copynumber: 2.2 Consensus size: 33
2687409 GTTCATTTAC
*
2687419 GTTCGTGAACGTTCGCTTATGTTCGCTCGATTAT
1 GTTCGT-AACGTTCACTTATGTTCGCTCGATTAT
* * * * *
2687453 GTTCGATTATGTTCATTTATGTTTGTTCGATTAT
1 GTTCG-TAACGTTCACTTATGTTCGCTCGATTAT
2687487 GTTCGT
1 GTTCGT
2687493 TTATGTTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 1 0.03
34 31 0.94
35 1 0.03
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (33 bp):
GTTCGTAACGTTCACTTATGTTCGCTCGATTAT
Found at i:2687458 original size:10 final size:10
Alignment explanation
Indices: 2687445--2687500 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 10
2687435 TTATGTTCGC
2687445 TCGATTATGT
1 TCGATTATGT
2687455 TCGATTATGT
1 TCGATTATGT
*
2687465 TC-ATT-T-A
1 TCGATTATGT
2687472 T-G-TT-TGT
1 TCGATTATGT
2687479 TCGATTATGT
1 TCGATTATGT
*
2687489 TCGTTTATGT
1 TCGATTATGT
2687499 TC
1 TC
2687501 ATTCATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
6 3 0.08
7 2 0.05
8 2 0.05
9 5 0.13
10 26 0.68
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (10 bp):
TCGATTATGT
Found at i:2687479 original size:24 final size:24
Alignment explanation
Indices: 2687452--2687499 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2687442 CGCTCGATTA
2687452 TGTTCGATTATGTTCATTTATGTT
1 TGTTCGATTATGTTCATTTATGTT
*
2687476 TGTTCGATTATGTTCGTTTATGTT
1 TGTTCGATTATGTTCATTTATGTT
2687500 CATTCATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.08, G:0.19, T:0.58
Consensus pattern (24 bp):
TGTTCGATTATGTTCATTTATGTT
Found at i:2687497 original size:34 final size:34
Alignment explanation
Indices: 2687435--2687503 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
2687425 GAACGTTCGC
2687435 TTATGTTCGCTCGATTATGTTCGATTATGTTCAT
1 TTATGTTCGCTCGATTATGTTCGATTATGTTCAT
* * *
2687469 TTATGTTTGTTCGATTATGTTCGTTTATGTTCAT
1 TTATGTTCGCTCGATTATGTTCGATTATGTTCAT
2687503 T
1 T
2687504 CATTTATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.16, C:0.12, G:0.17, T:0.55
Consensus pattern (34 bp):
TTATGTTCGCTCGATTATGTTCGATTATGTTCAT
Found at i:2687510 original size:24 final size:24
Alignment explanation
Indices: 2687454--2687513 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
2687444 CTCGATTATG
**
2687454 TTCGATTATGTTCATTTATGTTTG
1 TTCGATTATGTTCATTTATGTTCA
*
2687478 TTCGATTATGTTCGTTTATGTTCA
1 TTCGATTATGTTCATTTATGTTCA
2687502 TTC-ATTTATGTT
1 TTCGA-TTATGTT
2687514 TAACTCAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.58
Consensus pattern (24 bp):
TTCGATTATGTTCATTTATGTTCA
Found at i:2688605 original size:10 final size:10
Alignment explanation
Indices: 2688590--2688624 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
2688580 GTCTCGAACG
2688590 TTTATGTTCA
1 TTTATGTTCA
2688600 TTTATGTTCA
1 TTTATGTTCA
*
2688610 TTTATGTTCG
1 TTTATGTTCA
2688620 TTTAT
1 TTTAT
2688625 TTATTAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (10 bp):
TTTATGTTCA
Found at i:2699566 original size:42 final size:42
Alignment explanation
Indices: 2699520--2699607 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
2699510 TTAGATGTTT
* * * * *
2699520 GTTCTCAGTACTCAGCCGCTCGGTT-TCCACTTTTAAGAATCC
1 GTTCTCAGAACTCACCCGCTC-ATTCTCCAATTTTAACAATCC
*
2699562 GTTCTCAGAACTTACCCGCTCATTCTCCAATTTTAACAATCC
1 GTTCTCAGAACTCACCCGCTCATTCTCCAATTTTAACAATCC
2699604 GTTC
1 GTTC
2699608 ACACTACTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (42 bp):
GTTCTCAGAACTCACCCGCTCATTCTCCAATTTTAACAATCC
Found at i:2701930 original size:60 final size:59
Alignment explanation
Indices: 2701856--2701967 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 59
2701846 GTCACCAAGT
*
2701856 TATAACTCTCATTTTAAATT-GATTCTTAAACTTTTGAATATTCTAATTCTATCTCTAAAC
1 TATAACTCTCATTTTAAATTAG-TCCTTAAACTTTTGAA-ATTCTAATTCTATCTCTAAAC
* ** *
2701916 TATAACTTTCATTTTAAATTAGTCCTTAAGTTTTTGAAATTCTAATTTTATC
1 TATAACTCTCATTTTAAATTAGTCCTTAAACTTTTGAAATTCTAATTCTATC
2701968 CCAAATTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
59 13 0.28
60 32 0.70
61 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.49
Consensus pattern (59 bp):
TATAACTCTCATTTTAAATTAGTCCTTAAACTTTTGAAATTCTAATTCTATCTCTAAAC
Found at i:2701995 original size:59 final size:60
Alignment explanation
Indices: 2701856--2701999 Score: 145
Period size: 59 Copynumber: 2.4 Consensus size: 60
2701846 GTCACCAAGT
* ** *
2701856 TATAA-CTCTCATTTTAAATT-GATTCTTAAACTTTTGAATATTCTAATTCTATCTCTAAAC
1 TATAACCT-TCATTTTAAATTAG-TCCTTAAGTTTTTGAATATTCTAATTCTATCTCCAAAC
* * *
2701916 TATAACTTTCATTTTAAATTAGTCCTTAAGTTTTTGAA-ATTCTAATTTTATC-CCAAATT
1 TATAACCTTCATTTTAAATTAGTCCTTAAGTTTTTGAATATTCTAATTCTATCTCCAAA-C
*
2701975 TATGACCTTC-TTTCTAAATTAGTCC
1 TATAACCTTCATTT-TAAATTAGTCC
2702000 CCGAACTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
58 7 0.10
59 32 0.45
60 30 0.42
61 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (60 bp):
TATAACCTTCATTTTAAATTAGTCCTTAAGTTTTTGAATATTCTAATTCTATCTCCAAAC
Found at i:2706109 original size:3 final size:3
Alignment explanation
Indices: 2706096--2706137 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2706086 ATAAATAAGC
2706096 ATA AT- ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2706138 TACAATTAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:2706137 original size:14 final size:14
Alignment explanation
Indices: 2706070--2706137 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
2706060 CAAAAATTTG
*
2706070 TAATATATTAATAA
1 TAATATAATAATAA
* **
2706084 CAATA-AATAAGCA
1 TAATATAATAATAA
2706097 TAATATAATAATAA
1 TAATATAATAATAA
2706111 TAATAATAATAAT-A
1 TAAT-ATAATAATAA
2706125 TAATAATAATAAT
1 TAAT-ATAATAAT
2706138 TACAATTAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
13 9 0.20
14 28 0.62
15 8 0.18
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:2714994 original size:2 final size:2
Alignment explanation
Indices: 2714989--2715016 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2714979 TAATTAATTA
2714989 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
2715017 TATTGTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2715237 original size:41 final size:41
Alignment explanation
Indices: 2715180--2715257 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
2715170 GTATCACAAA
* *
2715180 TTCGCGTTGCGATAGTTGAAAACCGCGTTGCGGTTTTTCAT
1 TTCGCGTTGCAATAGTTGAAAACCGCGTTGCGATTTTTCAT
**
2715221 TTCGCGTTGCAATAGTTGAAAATTGCGTTGCGATTTT
1 TTCGCGTTGCAATAGTTGAAAACCGCGTTGCGATTTT
2715258 CCAAATTCGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (41 bp):
TTCGCGTTGCAATAGTTGAAAACCGCGTTGCGATTTTTCAT
Found at i:2715274 original size:19 final size:20
Alignment explanation
Indices: 2715240--2715334 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 20
2715230 CAATAGTTGA
2715240 AAATTGCGTTGCGATTTTCC
1 AAATTGCGTTGCGATTTTCC
*
2715260 AAATT-CGTTGTGATTTTCC
1 AAATTGCGTTGCGATTTTCC
* ** *
2715279 -ATTTCGCGTTGCGATAGTCT
1 AAATT-GCGTTGCGATTTTCC
* * *
2715299 ACAGTTGTCGCTACGATTTTCC
1 A-AATTG-CGTTGCGATTTTCC
2715321 AAATT-CGTTGCGAT
1 AAATTGCGTTGCGAT
2715335 AGTCCAAAAA
Statistics
Matches: 55, Mismatches: 15, Indels: 11
0.68 0.19 0.14
Matches are distributed among these distances:
18 3 0.05
19 20 0.36
20 15 0.27
21 4 0.07
22 13 0.24
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
AAATTGCGTTGCGATTTTCC
Found at i:2715282 original size:60 final size:61
Alignment explanation
Indices: 2715213--2715330 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 61
2715203 CGCGTTGCGG
* * *
2715213 TTTTTCATTTCGCGTTGCAATAGT-TGAAAATTG-CGTTGCGATTTTCCAAATTCGTTGTGA
1 TTTTCCATTTCGCGTTGCAATAGTCT-AAAATTGTCGCTACGATTTTCCAAATTCGTTGTGA
* * *
2715273 TTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGCTACGATTTTCCAAATTCGTTG
1 TTTTCCATTTCGCGTTGCAATAGTCTAAAATTGTCGCTACGATTTTCCAAATTCGTTG
2715331 CGATAGTCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
60 27 0.54
61 23 0.46
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (61 bp):
TTTTCCATTTCGCGTTGCAATAGTCTAAAATTGTCGCTACGATTTTCCAAATTCGTTGTGA
Found at i:2716170 original size:19 final size:19
Alignment explanation
Indices: 2716143--2716184 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2716133 ATAATATTAT
2716143 TAAAACTTGTTCTAAATTC
1 TAAAACTTGTTCTAAATTC
*
2716162 TAAACCTTGTTCTAAATTC
1 TAAAACTTGTTCTAAATTC
2716181 TAAA
1 TAAA
2716185 TCATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (19 bp):
TAAAACTTGTTCTAAATTC
Found at i:2716264 original size:26 final size:26
Alignment explanation
Indices: 2716235--2716315 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
2716225 GGAACAAGTG
2716235 TTGGTAATGCTCAATCCCACATAGTT
1 TTGGTAATGCTCAATCCCACATAGTT
* * * *** *
2716261 TTGGAAATACT-ATTGGGAACA-AGTG
1 TTGGTAATGCTCAAT-CCCACATAGTT
2716286 TTGGTAATGCTCAATCCCACATAGTT
1 TTGGTAATGCTCAATCCCACATAGTT
2716312 TTGG
1 TTGG
2716316 AAACACTATT
Statistics
Matches: 38, Mismatches: 14, Indels: 6
0.66 0.24 0.10
Matches are distributed among these distances:
25 17 0.45
26 21 0.55
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (26 bp):
TTGGTAATGCTCAATCCCACATAGTT
Found at i:2716289 original size:25 final size:25
Alignment explanation
Indices: 2716215--2716289 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 25
2716205 CCAAATAAAT
*
2716215 AATACTATTGGGAACAAGTGTTGGT
1 AATACTATTGGGAACAAGTGTTGGA
* * *** *
2716240 AATGCTCAAT-CCCACATAGTTTTGGA
1 AATACT-ATTGGGAACA-AGTGTTGGA
2716266 AATACTATTGGGAACAAGTGTTGG
1 AATACTATTGGGAACAAGTGTTGG
2716290 TAATGCTCAA
Statistics
Matches: 34, Mismatches: 13, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (25 bp):
AATACTATTGGGAACAAGTGTTGGA
Found at i:2716290 original size:51 final size:51
Alignment explanation
Indices: 2716215--2716330 Score: 223
Period size: 51 Copynumber: 2.3 Consensus size: 51
2716205 CCAAATAAAT
2716215 AATACTATTGGGAACAAGTGTTGGTAATGCTCAATCCCACATAGTTTTGGA
1 AATACTATTGGGAACAAGTGTTGGTAATGCTCAATCCCACATAGTTTTGGA
2716266 AATACTATTGGGAACAAGTGTTGGTAATGCTCAATCCCACATAGTTTTGGA
1 AATACTATTGGGAACAAGTGTTGGTAATGCTCAATCCCACATAGTTTTGGA
*
2716317 AACACTATTGGGAA
1 AATACTATTGGGAA
2716331 TGGTATTTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (51 bp):
AATACTATTGGGAACAAGTGTTGGTAATGCTCAATCCCACATAGTTTTGGA
Found at i:2716433 original size:6 final size:5
Alignment explanation
Indices: 2716403--2716443 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
2716393 GCGCGCCGCC
2716403 GTCGG GTCGG GTCGG GTCGG GTCGTG GTCGTG GTCGTG GTC
1 GTCGG GTCGG GTCGG GTCGG GTCG-G GTCG-G GTCG-G GTC
2716444 TTTGTCTGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 19 0.54
6 16 0.46
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
GTCGG
Found at i:2717408 original size:68 final size:68
Alignment explanation
Indices: 2717299--2717428 Score: 260
Period size: 68 Copynumber: 1.9 Consensus size: 68
2717289 TGTGTTGCAG
2717299 GACCAAGCTATATATAGACGATTGCCATCATTTTCAAATGAGATACCATTTTAACGAAGAGAACA
1 GACCAAGCTATATATAGACGATTGCCATCATTTTCAAATGAGATACCATTTTAACGAAGAGAACA
2717364 CAA
66 CAA
2717367 GACCAAGCTATATATAGACGATTGCCATCATTTTCAAATGAGATACCATTTTAACGAAGAGA
1 GACCAAGCTATATATAGACGATTGCCATCATTTTCAAATGAGATACCATTTTAACGAAGAGA
2717429 TTATCTTAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (68 bp):
GACCAAGCTATATATAGACGATTGCCATCATTTTCAAATGAGATACCATTTTAACGAAGAGAACA
CAA
Found at i:2718848 original size:21 final size:19
Alignment explanation
Indices: 2718819--2718862 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
2718809 ATTTATTTTA
2718819 TTTTTATTTTAGGAAT-TATC
1 TTTTTATTTTA--AATGTATC
2718839 TTTTTAATTTTAAATGTATC
1 TTTTT-ATTTTAAATGTATC
2718859 TTTT
1 TTTT
2718863 AGGGTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 13 0.59
21 6 0.27
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTTTATTTTAAATGTATC
Found at i:2722320 original size:26 final size:28
Alignment explanation
Indices: 2722291--2722351 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2722281 TTGATTATTT
* *
2722291 ATTTTATTAATA-GTAT-TCATTTTAAA
1 ATTTTATTAATACATATCTCATTTAAAA
*
2722317 ATTTTATTTATACATATCTCATTTAAAA
1 ATTTTATTAATACATATCTCATTTAAAA
2722345 ATTTTAT
1 ATTTTAT
2722352 ATACTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 11 0.37
27 3 0.10
28 16 0.53
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTTATTAATACATATCTCATTTAAAA
Found at i:2722345 original size:28 final size:26
Alignment explanation
Indices: 2722291--2722361 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 26
2722281 TTGATTATTT
* *
2722291 ATTTTATTAATAGTATTCATTTTAAA
1 ATTTTATTAATAATATTCATTTAAAA
*
2722317 ATTTTATTTATACATATCTCATTTAAAA
1 ATTTTATTAATA-ATAT-TCATTTAAAA
*
2722345 ATTTTATATACTAATAT
1 ATTTTAT-TAATAATAT
2722362 ATATATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 11 0.30
27 3 0.08
28 20 0.54
29 3 0.08
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (26 bp):
ATTTTATTAATAATATTCATTTAAAA
Found at i:2722363 original size:2 final size:2
Alignment explanation
Indices: 2722349--2722394 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
2722339 TTAAAAATTT
2722349 TA TA TA CTA -A TA TA TA 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 TA TA TA TA TA TA TA TA
2722391 TA TA
1 TA TA
2722395 ACCTAAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2722995 original size:2 final size:2
Alignment explanation
Indices: 2722988--2723026 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2722978 TTTTATGATC
2722988 AT 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 AT A
2723027 ACAATACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2724278 original size:3 final size:3
Alignment explanation
Indices: 2724272--2724324 Score: 56
Period size: 3 Copynumber: 17.0 Consensus size: 3
2724262 CACCCCCAGG
2724272 TCT TCT TCT TCT TCCT TCAT TCT T-T AT-T TCTT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT T-CT TC-T TCT TCT -TCT TC-T TCT TCT TCT TCT TCT
2724319 TCT TCT
1 TCT TCT
2724325 AAGTTTTAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.04
3 34 0.76
4 9 0.20
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:2725093 original size:18 final size:17
Alignment explanation
Indices: 2725066--2725100 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2725056 GAGGAAGAAG
2725066 AAGAAGGAAGAAGAAAGA
1 AAGAAGGAAGAA-AAAGA
*
2725084 AAGAATGAAGAAAAAGA
1 AAGAAGGAAGAAAAAGA
2725101 CCTGGGGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (17 bp):
AAGAAGGAAGAAAAAGA
Found at i:2725983 original size:3 final size:3
Alignment explanation
Indices: 2725975--2726042 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
2725965 GTTGTGCAAC
2725975 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2726022 AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG
2726043 GGGGAGTTAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2730223 original size:31 final size:33
Alignment explanation
Indices: 2730156--2730226 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 33
2730146 AGTGACCATT
*
2730156 TGTGTAGTTTACCTTTTTCTAACGTGGTAGTCAAC
1 TGTGTAGTTTACCTTTTTCAAAC--GGTAGTCAAC
*
2730191 TGTGTAGTTTACCTTTTTCAAAC-G-CGTCAAC
1 TGTGTAGTTTACCTTTTTCAAACGGTAGTCAAC
2730222 TGTGT
1 TGTGT
2730227 TTTTTGTCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 11 0.32
32 1 0.03
35 22 0.65
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (33 bp):
TGTGTAGTTTACCTTTTTCAAACGGTAGTCAAC
Found at i:2738257 original size:21 final size:21
Alignment explanation
Indices: 2738232--2738279 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2738222 CCTAATATTG
2738232 CAATGTCAAAATTAGATGCAA
1 CAATGTCAAAATTAGATGCAA
*
2738253 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGATGCAA
*
2738274 TAATGT
1 CAATGT
2738280 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGATGCAA
Found at i:2742910 original size:21 final size:21
Alignment explanation
Indices: 2742884--2742930 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2742874 CTAATATTGC
2742884 AATGTCAAAATTAGGTGCAAT
1 AATGTCAAAATTAGGTGCAAT
2742905 AATGTCAAAATTAGGTGCAAT
1 AATGTCAAAATTAGGTGCAAT
2742926 AATGT
1 AATGT
2742931 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (21 bp):
AATGTCAAAATTAGGTGCAAT
Found at i:2744044 original size:23 final size:23
Alignment explanation
Indices: 2743980--2744037 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
2743970 TCCGTCTAGG
2743980 TATAATATAGTGTAATTTTTTAA
1 TATAATATAGTGTAATTTTTTAA
2744003 TATAATATAGTGTAATTTTTTAA
1 TATAATATAGTGTAATTTTTTAA
2744026 TATAATATAGTG
1 TATAATATAGTG
2744038 CAGTTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (23 bp):
TATAATATAGTGTAATTTTTTAA
Found at i:2748828 original size:20 final size:20
Alignment explanation
Indices: 2748805--2748856 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2748795 AACGCGATCC
2748805 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2748825 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2748845 CCAAAATCGCAA
1 CCAGAATCGCAA
2748857 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2748937 original size:20 final size:20
Alignment explanation
Indices: 2748912--2749105 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
2748902 GATTTTCCAT
* *
2748912 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2748932 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2748952 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2748972 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2748992 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2749012 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2749032 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2749052 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2749073 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2749093 AATCGCAACGCGA
1 AATCGCAACGCGA
2749106 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2748957 original size:40 final size:39
Alignment explanation
Indices: 2748908--2749105 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
2748898 TTGCGATTTT
* ** *
2748908 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
2748946 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
2748987 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
2749027 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
2749066 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
2749106 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:2748995 original size:60 final size:60
Alignment explanation
Indices: 2748912--2749104 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2748902 GATTTTCCAT
* ** * *
2748912 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2748972 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2749032 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2749093 AATCGCAACGCG
1 AATCGCAACGCG
2749105 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2749525 original size:33 final size:33
Alignment explanation
Indices: 2749486--2749556 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2749476 TTCACTTAGA
*
2749486 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2749519 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2749552 TTTCA
1 TTTCA
2749557 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2749695 original size:14 final size:14
Alignment explanation
Indices: 2749676--2749730 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2749666 AGAATGACTG
2749676 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2749690 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2749709 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2749723 TCGCAACG
1 TCGCAACG
2749731 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2749713 original size:33 final size:33
Alignment explanation
Indices: 2749676--2749746 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2749666 AGAATGACTG
**
2749676 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2749709 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2749742 TCGCA
1 TCGCA
2749747 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2749783 original size:14 final size:14
Alignment explanation
Indices: 2749764--2749820 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
2749754 TTTCATTTCG
2749764 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2749778 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2749795 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2749811 CGTTGCGATT
1 CGTTGCGATT
2749821 TTCATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 5 0.13
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2749798 original size:33 final size:33
Alignment explanation
Indices: 2749747--2749825 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
2749737 CAAAATCGCA
*
2749747 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATCTCGCGTTGCGATTCTCTCG
*
2749780 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATCTCGCGTTGCGATTCTCTCG
2749813 TTGCGATTTTCAT
1 TTGCGATTTTCAT
2749826 TTCAACCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATCTCGCGTTGCGATTCTCTCG
Found at i:2749800 original size:19 final size:18
Alignment explanation
Indices: 2749742--2749821 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 18
2749732 GAAACCAAAA
* *
2749742 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
2749761 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
2749777 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
2749794 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
2749810 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
2749822 TCATTTCAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
14 16 0.30
15 3 0.06
16 7 0.13
17 8 0.15
18 1 0.02
19 18 0.34
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:2751751 original size:185 final size:186
Alignment explanation
Indices: 2751518--2751983 Score: 909
Period size: 185 Copynumber: 2.5 Consensus size: 186
2751508 TAGATTGCTT
*
2751518 AGTAAATTTATTCGGTTGCTG-CAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2751582 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2751647 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2751702 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2751767 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2751832 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2751888 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2751953 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
2751984 TTCAATTTGC
Statistics
Matches: 279, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 20 0.07
185 133 0.48
186 126 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2751831 original size:93 final size:93
Alignment explanation
Indices: 2751518--2751983 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
2751508 TAGATTGCTT
*
2751518 AGTAAATTTATTCGGTTGCTG-CAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2751582 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2751610 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2751674 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2751702 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2751767 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2751795 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2751860 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2751888 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2751953 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2751981 AGT
1 AGT
2751984 TTCAATTTGC
Statistics
Matches: 371, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 112 0.30
93 259 0.70
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2752055 original size:19 final size:19
Alignment explanation
Indices: 2752015--2752143 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2752005 TAGTTTACTT
* *
2752015 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2752035 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2752054 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2752073 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2752087 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2752106 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2752120 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2752139 TCGCA
1 TCGCA
2752144 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2752094 original size:33 final size:32
Alignment explanation
Indices: 2752051--2752143 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2752041 CGCGAAACCA
**
2752051 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2752083 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2752116 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2752144 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2752141 original size:52 final size:52
Alignment explanation
Indices: 2752015--2752143 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2752005 TAGTTTACTT
**
2752015 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2752067 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2752120 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2752144 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2752161 original size:19 final size:19
Alignment explanation
Indices: 2752139--2752259 Score: 135
Period size: 19 Copynumber: 6.6 Consensus size: 19
2752129 GAAACCAAAA
*
2752139 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2752158 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2752177 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2752193 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2752210 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2752229 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2752249 TCGTGTTGCGA
1 TCGCGTTGCGA
2752260 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
17 5 0.06
19 57 0.66
20 12 0.14
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2754197 original size:14 final size:14
Alignment explanation
Indices: 2754178--2754213 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2754168 ATTGTTTAAT
2754178 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2754192 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2754206 TGATTTGT
1 TGATTTGT
2754214 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2754335 original size:19 final size:19
Alignment explanation
Indices: 2754319--2754420 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2754309 AAAAATGACT
2754319 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2754338 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2754357 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2754371 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2754390 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2754410 ATCGCAATGCG
1 ATCGCAATGCG
2754421 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2754469 original size:33 final size:35
Alignment explanation
Indices: 2754427--2754701 Score: 267
Period size: 33 Copynumber: 7.9 Consensus size: 35
2754417 TGCGTTTATA
*
2754427 ATTTCGCATTGCGA-TT-ATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGTTGCGATTTTC
2754460 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG--TTGCGATTTTC
*
2754496 -TTTCG--TTGCGATTTTCATTTGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTT-CGTTGCGATTTTC
*
2754528 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA-TTTCATTTCG--TTGCGATTTTC
*
2754563 ATTTCGCATTGCGA-TTC-TGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGTTGCGATTTTC
2754596 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTTCG--TTGCGATTTTC
*
2754634 ATTTCGCATTGCGA-TTC-TCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGTTGCGATTTTC
2754667 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 ATTTCGCATTGCGA-TTTCATTTCG--TTGCGATT
2754702 CTCTCGTTGC
Statistics
Matches: 210, Mismatches: 9, Indels: 41
0.81 0.03 0.16
Matches are distributed among these distances:
31 1 0.00
32 29 0.14
33 84 0.40
34 1 0.00
35 23 0.11
36 27 0.13
38 45 0.21
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (35 bp):
ATTTCGCATTGCGATTTCATTTCGTTGCGATTTTC
Found at i:2754473 original size:19 final size:19
Alignment explanation
Indices: 2754449--2754768 Score: 360
Period size: 19 Copynumber: 18.4 Consensus size: 19
2754439 GATTATCTCG
2754449 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2754468 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2754487 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2754501 TTGCGATTTTCATTT-GCA
1 TTGCGATTTTCATTTCGCA
2754519 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2754533 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2754552 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2754571 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
2754585 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2754604 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2754623 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2754642 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2754656 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2754675 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2754694 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2754708 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2754728 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2754742 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2754761 TTGCGATT
1 TTGCGATT
2754769 GTATTTTCCG
Statistics
Matches: 259, Mismatches: 10, Indels: 64
0.78 0.03 0.19
Matches are distributed among these distances:
14 41 0.16
15 3 0.01
16 39 0.15
17 30 0.12
18 9 0.03
19 125 0.48
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2754489 original size:52 final size:52
Alignment explanation
Indices: 2754427--2754740 Score: 403
Period size: 52 Copynumber: 6.0 Consensus size: 52
2754417 TGCGTTTATA
*
2754427 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2754479 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTT-GCATTGCGA--TTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
2754528 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
2754584 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2754634 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2754686 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2754739 AT
1 AT
2754741 GTTGGGATTT
Statistics
Matches: 231, Mismatches: 14, Indels: 33
0.83 0.05 0.12
Matches are distributed among these distances:
46 6 0.03
48 8 0.03
49 8 0.03
50 9 0.04
51 28 0.12
52 140 0.61
53 17 0.07
54 2 0.01
55 1 0.00
56 4 0.02
57 4 0.02
58 1 0.00
59 3 0.01
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2754506 original size:14 final size:14
Alignment explanation
Indices: 2754487--2754540 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
2754477 TCATTTCGCA
2754487 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
*
2754501 TTGCGATTTTCATTTGCA
1 TTGCGA--TTC-TTT-CG
2754519 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
2754533 TTGCGATT
1 TTGCGATT
2754541 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 15 0.44
15 3 0.09
16 6 0.18
17 3 0.09
18 7 0.21
ACGTcount: A:0.11, C:0.19, G:0.20, T:0.50
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:2754541 original size:26 final size:27
Alignment explanation
Indices: 2754479--2754546 Score: 66
Period size: 32 Copynumber: 2.3 Consensus size: 27
2754469 TGCGATTTTC
2754479 ATTTCGCATTGCGATTCTTTCGTTGCGATTTT
1 ATTT-GCATTGCGATTCTTTCGTTGCG----T
2754511 CATTTGCATTGCGATTCTTTCGTTGCG-
1 -ATTTGCATTGCGATTCTTTCGTTGCGT
*
2754538 ATTTTCATT
1 ATTTGCATT
2754547 TCGCATTGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 8 0.24
32 22 0.65
33 4 0.12
ACGTcount: A:0.13, C:0.19, G:0.18, T:0.50
Consensus pattern (27 bp):
ATTTGCATTGCGATTCTTTCGTTGCGT
Found at i:2754624 original size:71 final size:71
Alignment explanation
Indices: 2754411--2754701 Score: 397
Period size: 71 Copynumber: 4.2 Consensus size: 71
2754401 GAAATGAAAA
* *
2754411 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
2754475 TTTCATT
65 TTTCATT
* * *
2754482 TCGCATTGCGA--TT-CTTTCG--TTGCGATTTTCATTTGCATTGCGA--TTC-TTTCG--TTGC
1 TCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TCT-CGTTGCGATTTTCATTTCGCATTGC
2754537 GATTTTCATT
62 GATTTTCATT
*
2754547 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
2754612 TTCATT
66 TTCATT
*
2754618 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
2754683 TTCATT
66 TTCATT
2754689 TCGCATTGCGATT
1 TCGCATTGCGATT
2754702 CTCTCGTTGC
Statistics
Matches: 195, Mismatches: 10, Indels: 30
0.83 0.04 0.13
Matches are distributed among these distances:
65 25 0.13
66 13 0.07
67 9 0.05
68 21 0.11
69 8 0.04
70 14 0.07
71 105 0.54
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (71 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
TTCATT
Found at i:2757062 original size:13 final size:13
Alignment explanation
Indices: 2757044--2757068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2757034 CTTCGGGGAC
2757044 TTTTTCTTCTTCT
1 TTTTTCTTCTTCT
2757057 TTTTTCTTCTTC
1 TTTTTCTTCTTC
2757069 AGGATTATAT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCTTCTTCT
Found at i:2757274 original size:24 final size:24
Alignment explanation
Indices: 2757240--2757286 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2757230 TCTGAAACTC
2757240 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2757264 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2757287 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2757991 original size:20 final size:20
Alignment explanation
Indices: 2757963--2758330 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
2757953 AAATTTCAGT
* * * *
2757963 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2757983 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2758003 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2758023 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2758043 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2758063 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2758083 GTTGCGATTTACGGAT-CGC
1 GTTGCGATTTACGGATACGC
2758102 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2758122 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2758142 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2758162 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2758182 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2758202 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2758222 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2758242 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2758262 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2758282 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2758302 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2758322 GTTGCGATT
1 GTTGCGATT
2758331 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
19 21 0.07
20 281 0.92
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2759237 original size:20 final size:20
Alignment explanation
Indices: 2759143--2759509 Score: 431
Period size: 20 Copynumber: 18.4 Consensus size: 20
2759133 GATTTTCCAT
* ** *
2759143 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2759163 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2759183 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2759203 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2759223 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2759243 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2759263 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2759283 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2759303 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2759323 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2759343 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2759363 AA-CGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2759382 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
2759402 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2759422 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
** *
2759442 AATCGCAACG-AAATCTGTA
1 AATCGCAACGCGTATCCGTA
* *
2759461 AATCGCAACG-ATAATCTGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2759481 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2759501 AATCACAAC
1 AATCGCAAC
2759510 ACTGAAATTT
Statistics
Matches: 307, Mismatches: 32, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
19 38 0.12
20 266 0.87
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2760228 original size:24 final size:24
Alignment explanation
Indices: 2760189--2760235 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2760179 AAATTTGGTC
2760189 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2760213 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2760236 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2762734 original size:19 final size:18
Alignment explanation
Indices: 2762710--2763019 Score: 335
Period size: 19 Copynumber: 18.1 Consensus size: 18
2762700 AAATCCCAAC
2762710 ATGAAATCGCAATGCGGAA
1 ATGAAATCGCAATGC-GAA
*
2762729 ATGAAAATCGCAA--CGAG
1 ATG-AAATCGCAATGCGAA
2762746 A-G-AATCGCAATGCGAA
1 ATGAAATCGCAATGCGAA
2762762 ATGAAAATCGCAATGCGAA
1 ATG-AAATCGCAATGCGAA
*
2762781 ATGAAAATCGCAA--CGAG
1 ATG-AAATCGCAATGCGAA
2762798 A-G-AATCGCAATGCGAA
1 ATGAAATCGCAATGCGAA
2762814 ATGAAAATCGCAATGCGAA
1 ATG-AAATCGCAATGCGAA
2762833 ATGAAATCGCAATGCGAA
1 ATGAAATCGCAATGCGAA
*
2762851 ATGAAATCGCAA--CGAC
1 ATGAAATCGCAATGCGAA
2762867 A-G-AATCGCAATGCGAA
1 ATGAAATCGCAATGCGAA
*
2762883 ATTAAAATCGCAATGCGAA
1 A-TGAAATCGCAATGCGAA
2762902 ATGAAATCGCAA--CGAA
1 ATGAAATCGCAATGCGAA
2762918 A-G-AATCGCAATGCGAA
1 ATGAAATCGCAATGCGAA
2762934 ATGAAAATCGCAA--CGAA
1 ATG-AAATCGCAATGCGAA
2762951 A-G-AATCGCAATGCGAA
1 ATGAAATCGCAATGCGAA
2762967 ATGAAAATCGCAATGCGAA
1 ATG-AAATCGCAATGCGAA
*
2762986 ATGAAATCGCAA--CGAG
1 ATGAAATCGCAATGCGAA
2763002 AT--AATCGCAATGCGAA
1 ATGAAATCGCAATGCGAA
2763018 AT
1 AT
2763020 TATAAACGCA
Statistics
Matches: 253, Mismatches: 10, Indels: 59
0.79 0.03 0.18
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 44 0.17
17 16 0.06
18 47 0.19
19 87 0.34
20 9 0.04
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (18 bp):
ATGAAATCGCAATGCGAA
Done.