Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 78
Found at i:2481358 original size:15 final size:15
Alignment explanation
Indices: 2481323--2481359 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2481313 CGTTTTTCCA
2481323 TCATTTTTCTTTTCT
1 TCATTTTTCTTTTCT
2481338 TC-TTTTTCTTCTTC-
1 TCATTTTTCTT-TTCT
2481352 TCATTTTT
1 TCATTTTT
2481360 ATTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (15 bp):
TCATTTTTCTTTTCT
Found at i:2490982 original size:45 final size:45
Alignment explanation
Indices: 2490915--2491065 Score: 221
Period size: 45 Copynumber: 3.3 Consensus size: 45
2490905 CCATGCTTTG
* *
2490915 TTATTCACAAAAATAAATCCTAACCTCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
*
2490962 TTATTCAAAAAATAAACCTAACCGCAAGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
*
2491007 TTATTTAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
*
2491052 ATTTATTCGAAAAA
1 --TTATTCAAAAAA
2491066 CGAAAATAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
45 69 0.73
46 9 0.09
47 17 0.18
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
Found at i:2492607 original size:18 final size:18
Alignment explanation
Indices: 2492586--2492623 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2492576 CATTATGACT
*
2492586 TATACATACA-TATATATA
1 TATACACACACTA-ATATA
2492604 TATACACACACTAATATA
1 TATACACACACTAATATA
2492622 TA
1 TA
2492624 ATGTACGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (18 bp):
TATACACACACTAATATA
Found at i:2496937 original size:15 final size:15
Alignment explanation
Indices: 2496919--2496955 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
2496909 ATCATATGAA
*
2496919 ATGTGATAAAGAGCT
1 ATGTGATAAAGAACT
2496934 ATGTG--AAAGAACT
1 ATGTGATAAAGAACT
2496947 ATGTGATAA
1 ATGTGATAA
2496956 TATGTGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 12 0.63
15 7 0.37
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.27
Consensus pattern (15 bp):
ATGTGATAAAGAACT
Found at i:2501108 original size:17 final size:17
Alignment explanation
Indices: 2501083--2501124 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
2501073 AACTCCCCCT
*
2501083 TTCTGCTTTTATATATA
1 TTCTTCTTTTATATATA
2501100 TTCTTCTTTTATATATA
1 TTCTTCTTTTATATATA
2501117 TTCTTCTT
1 TTCTTCTT
2501125 GGTGCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.14, G:0.02, T:0.64
Consensus pattern (17 bp):
TTCTTCTTTTATATATA
Found at i:2504677 original size:3 final size:3
Alignment explanation
Indices: 2504664--2504734 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
2504654 ACGTTTTAAA
* * *
2504664 TAT TAAT TAT TAT TA- TAT GAT TAAT TAT TAT TAA TAT T-T TAG TAT
1 TAT T-AT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
*
2504709 TAT TAT TA- TAT GAT TAAT TAT TAT TA
1 TAT TAT TAT TAT TAT T-AT TAT TAT TA
2504735 ATCGATCGAG
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
2 6 0.11
3 39 0.72
4 9 0.17
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:2504688 original size:18 final size:18
Alignment explanation
Indices: 2504665--2504734 Score: 97
Period size: 18 Copynumber: 3.8 Consensus size: 18
2504655 CGTTTTAAAT
2504665 ATTAATTATTATTATATG
1 ATTAATTATTATTATATG
2504683 ATTAATTATTATTAATAT-
1 ATTAATTATTATT-ATATG
*
2504701 TTTAGTATTATTATTATATG
1 ATTA--ATTATTATTATATG
2504721 ATTAATTATTATTA
1 ATTAATTATTATTA
2504735 ATCGATCGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
18 26 0.57
19 8 0.17
20 12 0.26
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
ATTAATTATTATTATATG
Found at i:2509724 original size:35 final size:35
Alignment explanation
Indices: 2509685--2509756 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
2509675 TGATGACAAA
*
2509685 GAAGCTTTAATGCATTTATGTTATATGTACAATTT
1 GAAGCTTAAATGCATTTATGTTATATGTACAATTT
2509720 GAAGCTTAAATGCATTTATGTTATATGTACAATTT
1 GAAGCTTAAATGCATTTATGTTATATGTACAATTT
2509755 GA
1 GA
2509757 TTCATGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (35 bp):
GAAGCTTAAATGCATTTATGTTATATGTACAATTT
Found at i:2511000 original size:25 final size:25
Alignment explanation
Indices: 2510954--2511026 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 25
2510944 AAAAATCACT
* *
2510954 AAGAATTATAAATAATACTAAAA-CTA
1 AAGAAATATAAA-AA-AATAAAAGCTA
2510980 GAAGAAATATAAAAAAATAAAAGCTA
1 -AAGAAATATAAAAAAATAAAAGCTA
* *
2511006 TAGAAA-ATTACAAAAATAAAA
1 AAGAAATA-TAAAAAAATAAAA
2511027 TAAAATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 1 0.03
25 23 0.57
26 5 0.12
27 11 0.28
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (25 bp):
AAGAAATATAAAAAAATAAAAGCTA
Found at i:2513297 original size:36 final size:31
Alignment explanation
Indices: 2513223--2513308 Score: 154
Period size: 31 Copynumber: 2.8 Consensus size: 31
2513213 GAGTATTACT
* *
2513223 GAGCTCGACTCGACTCGAAAATTTTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTGAAATG
2513254 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTGAAATG
2513285 GAGCTCGACTCGACTCGAAAACTC
1 GAGCTCGACTCGACTCGAAAACTC
2513309 GCGAGTTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (31 bp):
GAGCTCGACTCGACTCGAAAACTCTGAAATG
Found at i:2513628 original size:17 final size:17
Alignment explanation
Indices: 2513606--2513653 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
2513596 GGCTCGTTAA
2513606 GAACTCGAGTCGAGCTC
1 GAACTCGAGTCGAGCTC
2513623 GAACTCGAGTCGAGCTC
1 GAACTCGAGTCGAGCTC
2513640 -AAGCTCGAGTCGAG
1 GAA-CTCGAGTCGAG
2513654 TCAATTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 2 0.07
17 28 0.93
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.17
Consensus pattern (17 bp):
GAACTCGAGTCGAGCTC
Found at i:2514914 original size:41 final size:41
Alignment explanation
Indices: 2514356--2514907 Score: 923
Period size: 41 Copynumber: 13.5 Consensus size: 41
2514346 ATTCGCGTTG
*
2514356 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
2514397 CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
2514438 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
2514479 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
2514520 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
2514561 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
2514602 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
2514643 CATTTCGCGTTGCGATAGTTGAAAATCGAGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
2514684 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
* *
2514725 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
2514766 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
2514807 CATTTCGCGTTGCGATAGTTGTAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
2514848 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
*
2514889 CGTTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
2514908 CTACAGTTGT
Statistics
Matches: 488, Mismatches: 18, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
40 2 0.00
41 483 0.99
42 3 0.01
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:2514942 original size:24 final size:24
Alignment explanation
Indices: 2514910--2514958 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2514900 GCGATAGTCT
*
2514910 ACAGTTGTCGTTGCGATTTTCCAA
1 ACAGTTGTCATTGCGATTTTCCAA
2514934 ACAGTTGTCATTGCGATTTTCCAA
1 ACAGTTGTCATTGCGATTTTCCAA
2514958 A
1 A
2514959 TTCGTTGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (24 bp):
ACAGTTGTCATTGCGATTTTCCAA
Found at i:2515061 original size:6 final size:6
Alignment explanation
Indices: 2515050--2515144 Score: 162
Period size: 6 Copynumber: 16.5 Consensus size: 6
2515040 GACACGTATT
2515050 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2515098 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2515142 ACC
1 ACC
2515145 CGAGACGAGA
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 20 0.22
6 69 0.78
ACGTcount: A:0.31, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2515387 original size:20 final size:20
Alignment explanation
Indices: 2515362--2515434 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
2515352 GTCGTAGACT
2515362 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
2515382 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
2515403 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
2515423 AACGCAACGCGA
1 ATCGCAACGCGA
2515435 TCTCCAACTA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:2515416 original size:41 final size:41
Alignment explanation
Indices: 2515359--2515459 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
2515349 GTGGTCGTAG
* * *
2515359 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTCCA
2515400 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTCCA
1 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTCCA
*
2515441 ACTATCGCAATGCGAAATG
1 ACTATCGCAACGCGAAATG
2515460 CAACGTGAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.17
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTCCA
Found at i:2515463 original size:21 final size:21
Alignment explanation
Indices: 2515359--2515463 Score: 88
Period size: 21 Copynumber: 5.1 Consensus size: 21
2515349 GTGGTCGTAG
*
2515359 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
2515380 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
2515400 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
2515421 A-AAACGCAACGCGATCTCCA
1 ACTATCGCAACGCGAAATGCA
*
2515441 ACTATCGCAATGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
2515462 AC
1 AC
2515464 GTGAATTTGC
Statistics
Matches: 60, Mismatches: 22, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 31 0.52
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:2518262 original size:55 final size:54
Alignment explanation
Indices: 2518203--2518702 Score: 319
Period size: 55 Copynumber: 9.1 Consensus size: 54
2518193 GTCAGGATAA
*
2518203 ATAAGACTTGAAAAATCTTCAAATGACGAGCCTGCTCTCTATTCCTTCAG-GAAGT
1 ATAAGACTTGAAAAATCTTCAAA-AACGAGCCTGCTCTCTATTCCTTCAGAG-AGT
* * * * * * *
2518258 ATAAGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTATTCATTCAAAGAGT
1 ATAAGACTTGAAAAATCTTCA-AAAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
* *
2518313 ATAAGACTTGAATAATCTTCAATAAAACGGGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAGACTTGAAAAATCTTC-A-AAAACGAG-CCTGCTCTCTATTCCTTCAGAGAGT
* * * ** * *
2518369 AT-AGAAATCGGAAAATCTTCAATAAAC-AGGTTCGCTCCCTATTCTTTCAGAGAGT
1 ATAAG-ACTTGAAAAATCTTCAA-AAACGAGCCT-GCTCTCTATTCCTTCAGAGAGT
* * * * *
2518424 ATAGGAC-T---CAATCTTTAACAAACGTGTCC-GCTCCCTATTCCTTCAGAGAGT
1 ATAAGACTTGAAAAATCTTCAA-AAACGAG-CCTGCTCTCTATTCCTTCAGAGAGT
** *
2518475 AT-AGAACTTGAGCAATCTTCATAAAACGGGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAAAAATCTTCA-AAAACGAG-CCTGCTCTCTATTCCTTCAGAGAGT
* * * * *
2518530 AT-AGAACTCGAACAATCTTCAACAAACGTGTCAGCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAAAAATCTTCAA-AAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
* * * *
2518585 AT-AGAACTCGAACAATCTTCATGAAACGGGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAAAAATCTTCA-AAAACGAG-CCTGCTCTCTATTCCTTCAGAGAGT
* * * ** * * *
2518640 AT-AGAACTCGAACAATCTTCAACGAACTTGTCTGCTCCCTATTCCTTTAGAGAGT
1 ATAAG-ACTTGAAAAATCTTCAA-AAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
*
2518695 ATAGGACT
1 ATAAGACT
2518703 CAATCTTCAA
Statistics
Matches: 368, Mismatches: 53, Indels: 48
0.78 0.11 0.10
Matches are distributed among these distances:
50 1 0.00
51 37 0.10
52 2 0.01
54 5 0.01
55 274 0.74
56 48 0.13
57 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (54 bp):
ATAAGACTTGAAAAATCTTCAAAAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
Found at i:2518517 original size:161 final size:162
Alignment explanation
Indices: 2518269--2518698 Score: 514
Period size: 165 Copynumber: 2.6 Consensus size: 162
2518259 TAAGACTCGA
* * * * *
2518269 ACAATCTTCATA-AAATGTGTCTGCTCTCTATTCATTCAAAGAGTATA-AGACTTGAATAATCTT
1 ACAATCTTCA-ACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTTGAACAATCTT
*
2518332 CAATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAATCGGAA-AATCTTCAATAAAC
64 C-ATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAATC-GAACAATCTTCAACAAAC
* *
2518396 AG-GTTC-GCTCCCTATTCTTTCAGAGAGTATAGGACT
127 -GTG-TCAGCTCCCTATTCCTTCAGAGAGTATAGAACT
* * *
2518432 -CAATCTTTAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTTGAGCAATCTTCA
1 ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTTGAACAATCTTCA
*
2518496 TAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGT
66 TAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAATCGAACAATCTTCAACAAACGTGT
*
2518561 CAGCTCTCTATTCCTTCAGAGAGTATAGAACT
131 CAGCTCCCTATTCCTTCAGAGAGTATAGAACT
** * *
2518593 CGAACAATCTTCATGAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCT
1 ---ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTTGAACAATCT
* ** * * *
2518658 TCA-ACGAACTTGTCTGCTCCCTATTCCTTTAGAGAGTATAG
63 TCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAG
2518699 GACTCAATCT
Statistics
Matches: 231, Mismatches: 26, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
160 6 0.03
161 85 0.37
162 51 0.22
163 1 0.00
164 1 0.00
165 87 0.38
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (162 bp):
ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTTGAACAATCTTCA
TAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAATCGAACAATCTTCAACAAACGTGT
CAGCTCCCTATTCCTTCAGAGAGTATAGAACT
Found at i:2518586 original size:110 final size:110
Alignment explanation
Indices: 2518236--2518703 Score: 576
Period size: 110 Copynumber: 4.3 Consensus size: 110
2518226 TGACGAGCCT
* * *
2518236 GCTCTCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTA
1 GCTCTCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTA
* * * * * *
2518299 TTCATTCAAAGAGTATA-AGACTTGAATAATCTTCAATAAAACGGGTCC
64 TTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-CAAACGTGTCC
* * * *
2518347 GCTCTCTATTCCTTCAGAGAGTATAGAAATCGGAA-AATCTTCA-ATAAACAGGTTCGCTCCCTA
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCATA-AAACGGGTCCGCTCTCTA
* * *
2518410 TTCTTTCAGAGAGTATAGGACT----CAATCTTTAACAAACGTGTCC
64 TTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * *
2518453 GCTCCCTATTCCTTCAGAGAGTATAGAACTTGAGCAATCTTCATAAAACGGGTCCGCTCTCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
*
2518518 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCA
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
*
2518563 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCGCTCTCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* * *
2518628 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCT
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * *
2518673 GCTCCCTATTCCTTTAGAGAGTATAGGACTC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTC
2518704 AATCTTCAAC
Statistics
Matches: 311, Mismatches: 35, Indels: 23
0.84 0.09 0.06
Matches are distributed among these distances:
105 2 0.01
106 80 0.26
107 9 0.03
110 151 0.49
111 64 0.21
112 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (110 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
Found at i:2518719 original size:55 final size:52
Alignment explanation
Indices: 2518269--2518718 Score: 390
Period size: 55 Copynumber: 8.3 Consensus size: 52
2518259 TAAGACTCGA
* * * * *
2518269 ACAATCTTCATA-AAATGTGTCTGCTCTCTATTCATTCAAAGAGTATA-AGACTT
1 ACAATCTTCA-ACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-AC-T
* * * * *
2518322 GAATAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAATCGG
1 --ACAATCTTCAA-CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAG-AA-C-T
* * * * *
2518380 AAAATCTTCAATAAACAG-GTTCGCTCCCTATTCTTTCAGAGAGTATAGGACT
1 ACAATCTTCAACAAAC-GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
*
2518432 -CAATCTTTAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTT
1 ACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAAC-T
* *
2518484 GAGCAATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 -A-CAATCTTCA-ACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
* *
2518538 CGAACAATCTTCAACAAACGTGTCAGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
** * *
2518593 CGAACAATCTTCATGAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
* * * * *
2518648 CGAACAATCTTCAACGAACTTGTCTGCTCCCTATTCCTTTAGAGAGTATAGGACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
2518703 -CAATCTTCAACAAACG
1 ACAATCTTCAACAAACG
2518719 AGTACTCTTC
Statistics
Matches: 338, Mismatches: 42, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
50 1 0.00
51 56 0.17
52 1 0.00
53 1 0.00
54 4 0.01
55 229 0.68
56 43 0.13
57 1 0.00
58 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (52 bp):
ACAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
Found at i:2519034 original size:17 final size:17
Alignment explanation
Indices: 2519002--2519034 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2518992 TATGTTCATC
2519002 TCAATACTTCAATATCT
1 TCAATACTTCAATATCT
2519019 TCAAT-CTTCAACTATC
1 TCAATACTTCAA-TATC
2519035 CCTGTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (17 bp):
TCAATACTTCAATATCT
Found at i:2520175 original size:15 final size:15
Alignment explanation
Indices: 2520132--2520211 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 15
2520122 CCATTTTTTC
2520132 TCTTTTTT-TC-TTT
1 TCTTTTTTCTCATTT
2520145 TCGTTTTTTCCATCATTT
1 TC-TTTTTT-C-TCATTT
2520163 TCTTTTTTCTCATTTT
1 TCTTTTTTCTCA-TTT
2520179 TCTTTTCTTCT--TTT
1 TCTTTT-TTCTCATTT
*
2520193 TC-TTCTTCTCATTT
1 TCTTTTTTCTCATTT
2520207 T-TTTT
1 TCTTTT
2520212 ATTATTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
12 4 0.07
13 4 0.07
14 17 0.31
15 3 0.05
16 10 0.18
17 12 0.22
18 5 0.09
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (15 bp):
TCTTTTTTCTCATTT
Found at i:2520193 original size:40 final size:42
Alignment explanation
Indices: 2520116--2520194 Score: 110
Period size: 40 Copynumber: 1.9 Consensus size: 42
2520106 ATTTCTCTTC
*
2520116 CATTTTCCATTTTTTCTCTTTTTTTCTTTTCGTTTTTTCCAT
1 CATTTTCCATTTTTTCTCTATTTTTCTTTTCGTTTTTTCCAT
*
2520158 CATTTT-C-TTTTTTCTC-ATTTTTCTTTTCTTCTTTTTC
1 CATTTTCCATTTTTTCTCTATTTTTCTTTTCGT-TTTTTC
2520195 TTCTTCTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 12 0.35
40 15 0.44
41 1 0.03
42 6 0.18
ACGTcount: A:0.06, C:0.22, G:0.01, T:0.71
Consensus pattern (42 bp):
CATTTTCCATTTTTTCTCTATTTTTCTTTTCGTTTTTTCCAT
Found at i:2520221 original size:11 final size:10
Alignment explanation
Indices: 2520205--2520241 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
2520195 TTCTTCTCAT
*
2520205 TTTTTTTATTA
1 TTTTTTT-TCA
2520216 TTTTTTTTCA
1 TTTTTTTTCA
2520226 TTTTTTTTCA
1 TTTTTTTTCA
2520236 TTTTTT
1 TTTTTT
2520242 CTTTTTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:2520226 original size:22 final size:24
Alignment explanation
Indices: 2520191--2520248 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 24
2520181 TTTTCTTCTT
2520191 TTTCTTCTTCTCATTTTTTTT-ATTA
1 TTTCTT-TT-TCATTTTTTTTCATTA
*
2520216 TTT-TTTTTCATTTTTTTTCATTT
1 TTTCTTTTTCATTTTTTTTCATTA
2520239 TTTCTTTTTC
1 TTTCTTTTTC
2520249 TCTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 11 0.37
23 8 0.27
24 8 0.27
25 3 0.10
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTCTTTTTCATTTTTTTTCATTA
Found at i:2520252 original size:8 final size:7
Alignment explanation
Indices: 2520160--2520254 Score: 54
Period size: 7 Copynumber: 13.3 Consensus size: 7
2520150 TTTTCCATCA
2520160 TTTTCTT
1 TTTTCTT
2520167 TTTTCTCAT
1 TTTTCT--T
2520176 TTTTCTT
1 TTTTCTT
2520183 TTCTTC-T
1 TT-TTCTT
2520190 TTTTCTT
1 TTTTCTT
* *
2520197 CTTCTCAT
1 -TTTTCTT
2520205 TTTT-TT
1 TTTTCTT
* *
2520211 TATTATT
1 TTTTCTT
2520218 TTTT-TT
1 TTTTCTT
**
2520224 CATT-TT
1 TTTTCTT
2520230 TTTTCATT
1 TTTTC-TT
2520238 TTTTCTT
1 TTTTCTT
2520245 TTTCTCTT
1 TTT-TCTT
2520253 TT
1 TT
2520255 ATTTCTTCTT
Statistics
Matches: 69, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
6 15 0.22
7 26 0.38
8 21 0.30
9 7 0.10
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:2520254 original size:14 final size:15
Alignment explanation
Indices: 2520160--2520254 Score: 63
Period size: 14 Copynumber: 6.2 Consensus size: 15
2520150 TTTTCCATCA
2520160 TTTTCTTTTTTCTCAT
1 TTTTC-TTTTTCTCAT
2520176 TTTTC-TTTTCTTC-T
1 TTTTCTTTTTC-TCAT
*
2520190 TTTTCTTCTTCTCAT
1 TTTTCTTTTTCTCAT
* **
2520205 TTTT-TTTATTATTTT
1 TTTTCTTT-TTCTCAT
*
2520220 TTTTCATTTTTTTTCATT
1 TTTTC--TTTTTCTCA-T
2520238 TTTTCTTTTTCTC-T
1 TTTTCTTTTTCTCAT
2520252 TTT
1 TTT
2520255 ATTTCTTCTT
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
14 19 0.31
15 19 0.31
16 12 0.19
17 3 0.05
18 9 0.15
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCTTTTTCTCAT
Found at i:2520257 original size:40 final size:37
Alignment explanation
Indices: 2520126--2520261 Score: 105
Period size: 39 Copynumber: 3.5 Consensus size: 37
2520116 CATTTTCCAT
* * *
2520126 TTTTTCTCTTTTTTTCTTTTCGTTTTTTCCATCATTTTC
1 TTTTT-TCTTTTTTTCTTTTCTTTTTTTTCAT-TTTTTC
* * *
2520165 TTTTTTCTCATTTTTCTTTTCTTCTTTTTC-TTCTTCTC
1 TTTTTTCT-TTTTTTCTTTTCTTTTTTTTCATT-TTTTC
*
2520203 ATTTTTT-TTATTATTTTTTTTCATTTTTTTTCATTTTTTC
1 -TTTTTTCTT-TT-TTTCTTTTC-TTTTTTTTCATTTTTTC
2520243 TTTTTCTCTTTTATTTCTT
1 TTTTT-TCTTTT-TTTCTT
2520262 CTTCAAGCGA
Statistics
Matches: 77, Mismatches: 11, Indels: 17
0.73 0.10 0.16
Matches are distributed among these distances:
38 11 0.14
39 41 0.53
40 21 0.27
41 4 0.05
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.76
Consensus pattern (37 bp):
TTTTTTCTTTTTTTCTTTTCTTTTTTTTCATTTTTTC
Found at i:2529824 original size:50 final size:44
Alignment explanation
Indices: 2529769--2529874 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 44
2529759 TCCTACCCAA
2529769 CATGATATCTACCCCCATGCTTTGTTATTCACAAAAATAAATCCTAACCG
1 CATGATATCTACCCCCATGC-TTG---TTCA-AAAAATAAA-CCTAACCG
* ** *
2529819 CATGATATTTAATTCGCATGCTTGTTCAAAAAATAAACCTAACCG
1 CATGATATCT-ACCCCCATGCTTGTTCAAAAAATAAACCTAACCG
2529864 CATGATATCTA
1 CATGATATCTA
2529875 GTTCGCATGC
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
44 1 0.02
45 17 0.34
46 9 0.18
47 4 0.08
50 12 0.24
51 7 0.14
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (44 bp):
CATGATATCTACCCCCATGCTTGTTCAAAAAATAAACCTAACCG
Found at i:2529864 original size:45 final size:46
Alignment explanation
Indices: 2529793--2529895 Score: 163
Period size: 45 Copynumber: 2.2 Consensus size: 46
2529783 CCATGCTTTG
*
2529793 TTATTCACAAAAATAAATCCTAACCGCATGATATTTAATTCGCATGC
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
* *
2529840 TTGTTCAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
2529885 TTATTCAAAAA
1 TTATTCAAAAA
2529896 CGAAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 37 0.71
46 9 0.17
47 6 0.12
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
Found at i:2533913 original size:24 final size:24
Alignment explanation
Indices: 2533886--2533938 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2533876 GATTACAAGT
**
2533886 AAATTAGTGAAGGTGGAGTTGTGA
1 AAATTAGAAAAGGTGGAGTTGTGA
*
2533910 AAATCAGAAAAGGTGGAGTTGTGA
1 AAATTAGAAAAGGTGGAGTTGTGA
2533934 AAATT
1 AAATT
2533939 TGTCTAGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.32, T:0.26
Consensus pattern (24 bp):
AAATTAGAAAAGGTGGAGTTGTGA
Found at i:2536027 original size:31 final size:30
Alignment explanation
Indices: 2535985--2536103 Score: 132
Period size: 31 Copynumber: 3.9 Consensus size: 30
2535975 GAGTCGAGGG
*
2535985 TTACCTCTGTCTTTCGAGACATATGGACATA
1 TTACCTATGTCTTTCGAGACATATGGACA-A
*
2536016 TTACCTATGTCTTTCGAGACATATGGATAGA
1 TTACCTATGTCTTTCGAGACATATGGACA-A
** * * *
2536047 TTACCTATGTCCGTAGGGACATATGGACAG
1 TTACCTATGTCTTTCGAGACATATGGACAA
*
2536077 TTACCTATGT-TCTTCGAAACATATGGA
1 TTACCTATGTCT-TTCGAGACATATGGA
2536104 TAGTGGTCAT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
30 21 0.29
31 52 0.71
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (30 bp):
TTACCTATGTCTTTCGAGACATATGGACAA
Found at i:2537425 original size:11 final size:12
Alignment explanation
Indices: 2537405--2537430 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2537395 TATTTGATAT
2537405 ATCAATTTTTTA
1 ATCAATTTTTTA
2537417 ATCAATTTTTTA
1 ATCAATTTTTTA
2537429 AT
1 AT
2537431 ATTTCAAATT
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:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
ATCAATTTTTTA
Found at i:2543063 original size:43 final size:43
Alignment explanation
Indices: 2542962--2543073 Score: 100
Period size: 43 Copynumber: 2.6 Consensus size: 43
2542952 CCGCAATATG
* * *
2542962 TAGGCTTTGATATTTAGCGGCATTTTCCCCAAAAACGCCGCAA
1 TAGGTTTTGATATTTAGCGGCATTTTCCCCAAAAACGACGAAA
* * * * ***
2543005 TAGGTATTAAGATTTAGCGGTATTTT-TTTAACAAACGACGAAA
1 TAGGTTTTGATATTTAGCGGCATTTTCCCCAA-AAACGACGAAA
* *
2543048 TAGGTTTTGATATTTAACGGCGTTTT
1 TAGGTTTTGATATTTAGCGGCATTTT
2543074 TTTCTCACAA
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
42 2 0.04
43 50 0.96
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (43 bp):
TAGGTTTTGATATTTAGCGGCATTTTCCCCAAAAACGACGAAA
Found at i:2547358 original size:15 final size:15
Alignment explanation
Indices: 2547338--2547366 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2547328 CATCTAAATC
2547338 TATGGACAAACTCTA
1 TATGGACAAACTCTA
2547353 TATGGACAAACTCT
1 TATGGACAAACTCT
2547367 TCATCCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (15 bp):
TATGGACAAACTCTA
Found at i:2552823 original size:49 final size:49
Alignment explanation
Indices: 2552767--2552870 Score: 183
Period size: 49 Copynumber: 2.1 Consensus size: 49
2552757 AACACAATAA
2552767 TTTATAATGATTTGAATTTCTTAACAAAGTCTACATTCATTAT-TGTATC
1 TTTATAATGATTTGAATTTCTTAACAAAGTCTACATTCATTATCT-TATC
*
2552816 TTTATAATGATTTGAATTTCTTAACAAAGTCTACGTTCATTATCTTATC
1 TTTATAATGATTTGAATTTCTTAACAAAGTCTACATTCATTATCTTATC
2552865 TTTATA
1 TTTATA
2552871 TCACATAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
49 52 0.98
50 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (49 bp):
TTTATAATGATTTGAATTTCTTAACAAAGTCTACATTCATTATCTTATC
Found at i:2557330 original size:2 final size:2
Alignment explanation
Indices: 2557323--2557359 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2557313 CTTGAATTTA
2557323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2557360 TTATTTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2562097 original size:86 final size:86
Alignment explanation
Indices: 2561912--2562157 Score: 214
Period size: 86 Copynumber: 2.9 Consensus size: 86
2561902 CAATCTCATT
* * * * *
2561912 TTTTTACATTTATAATTGATGATCCTAA-ATTTTTCAAT-TCTACCTTGTACCTTTATAATTAAG
1 TTTTTACCTTTATAATTGATGACCCTAATTTTTTTCAATCTC-ACTTTTTACCTTTATAATTAAG
* * ** * *
2561975 CTCTTTCTTTTTTCAATCCCAT
65 CCCCTAATTTTTTCAATACCAC
* * * *
2561997 TTTTTA-CTCATATAATTTATGACCCTAATTTTTTTCAATCTCACTTTTTACCTTTAAAATTGAT
1 TTTTTACCT-TTATAATTGATGACCCTAATTTTTTTCAATCTCACTTTTTACCTTTATAATT-AA
2562061 GCCCCTAATTTTTT-AATACCAC
64 GCCCCTAATTTTTTCAATACCAC
** * ** * *
2562083 TTTTTACCTTTATAATTGGGGTCATTAATTTTTTTCAATCAT-ACTTTTTACTTTTATAGTTTAA
1 TTTTTACCTTTATAATTGATGACCCTAATTTTTTTCAATC-TCACTTTTTACCTTTATA-ATTAA
2562147 GCCCCTAATTT
64 GCCCCTAATTT
2562158 AATCCATTTT
Statistics
Matches: 128, Mismatches: 26, Indels: 13
0.77 0.16 0.08
Matches are distributed among these distances:
84 1 0.01
85 22 0.17
86 87 0.68
87 18 0.14
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.50
Consensus pattern (86 bp):
TTTTTACCTTTATAATTGATGACCCTAATTTTTTTCAATCTCACTTTTTACCTTTATAATTAAGC
CCCTAATTTTTTCAATACCAC
Found at i:2562156 original size:44 final size:44
Alignment explanation
Indices: 2561895--2562157 Score: 159
Period size: 44 Copynumber: 6.1 Consensus size: 44
2561885 CCTTAATTTT
* * * **
2561895 TTTTTTTCAATCTCATTTTTTTACATTTATAATTGATGATCCTAA
1 TTTTTTTCAATCACA-CTTTTTACCTTTATAATTGATGCCCCTAA
* * * * *
2561940 -ATTTTTCAATTCTAC-C-TTGTACCTTTATAATT-AAG-CTCT-T
1 TTTTTTTCAA-TC-ACACTTTTTACCTTTATAATTGATGCCCCTAA
* * * * *
2561980 TCTTTTTTCAATCCCATTTTTTA-CTCATATAATTTATGACCCTAA
1 T-TTTTTTCAATCACACTTTTTACCT-TTATAATTGATGCCCCTAA
* *
2562025 TTTTTTTCAATCTCACTTTTTACCTTTAAAATTGATGCCCCTAA
1 TTTTTTTCAATCACACTTTTTACCTTTATAATTGATGCCCCTAA
** * **
2562069 -TTTTTT-AAT-ACCACTTTTTACCTTTATAATTGGGGTCATTAA
1 TTTTTTTCAATCA-CACTTTTTACCTTTATAATTGATGCCCCTAA
* * * * *
2562111 TTTTTTTCAATCATACTTTTTACTTTTATAGTTTAAGCCCCTAA
1 TTTTTTTCAATCACACTTTTTACCTTTATAATTGATGCCCCTAA
2562155 TTT
1 TTT
2562158 AATCCATTTT
Statistics
Matches: 164, Mismatches: 39, Indels: 31
0.70 0.17 0.13
Matches are distributed among these distances:
40 1 0.01
41 6 0.04
42 49 0.30
43 28 0.17
44 73 0.45
45 6 0.04
46 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.51
Consensus pattern (44 bp):
TTTTTTTCAATCACACTTTTTACCTTTATAATTGATGCCCCTAA
Found at i:2564635 original size:20 final size:20
Alignment explanation
Indices: 2564610--2564649 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2564600 CCAGGGTAAG
2564610 TATTGATACT-TAAGGATCGA
1 TATTGATACTAT-AGGATCGA
2564630 TATTGATACTATAGGATCGA
1 TATTGATACTATAGGATCGA
2564650 GTATCGGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (20 bp):
TATTGATACTATAGGATCGA
Found at i:2567546 original size:21 final size:22
Alignment explanation
Indices: 2567515--2567556 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2567505 TTATACTTTA
2567515 ATTTAAAAATTCAAT-TAAAATG
1 ATTTAAAAATT-AATATAAAATG
2567537 ATTT-AAAATTAATATAAAAT
1 ATTTAAAAATTAATATAAAAT
2567557 TTAATATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 12 0.63
22 4 0.21
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTTAAAAATTAATATAAAATG
Found at i:2569788 original size:5 final size:5
Alignment explanation
Indices: 2569778--2569807 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2569768 TTAAAAGTAT
2569778 TATCA TATCA TATCA TATCA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA
2569808 CTACCTTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TATCA
Found at i:2574979 original size:14 final size:14
Alignment explanation
Indices: 2574962--2574988 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2574952 CAAGATATGG
2574962 GAGAGAGAAAAGTA
1 GAGAGAGAAAAGTA
2574976 GAGAGAGAAAAGT
1 GAGAGAGAAAAGT
2574989 TAAAAGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
GAGAGAGAAAAGTA
Found at i:2575188 original size:17 final size:19
Alignment explanation
Indices: 2575166--2575200 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2575156 GCTTTTGTTC
2575166 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
2575183 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
2575201 GAGATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:2595599 original size:21 final size:21
Alignment explanation
Indices: 2595561--2595612 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2595551 CTTATTATAT
*
2595561 AAAATTAAT-TTAATAAAATA
1 AAAAATAATATTAATAAAATA
2595581 AATAAATAATATTAA-AAAATA
1 AA-AAATAATATTAATAAAATA
*
2595602 AAAAAAAATAT
1 AAAAATAATAT
2595613 ATTAACAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
21 14 0.50
22 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATAATATTAATAAAATA
Found at i:2595614 original size:22 final size:22
Alignment explanation
Indices: 2595570--2595617 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
2595560 TAAAATTAAT
* *
2595570 TTAATAAAATAAATAAATAATA
1 TTAATAAAATAAAAAAAAAATA
2595592 TTAA-AAAATAAAAAAAAATATA
1 TTAATAAAATAAAAAAAAA-ATA
2595614 TTAA
1 TTAA
2595618 CAATATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TTAATAAAATAAAAAAAAAATA
Found at i:2595710 original size:24 final size:24
Alignment explanation
Indices: 2595681--2595735 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
2595671 TAGACACATA
2595681 ACATGTGTCACATCATTATTTTAT
1 ACATGTGTCACATCATTATTTTAT
*
2595705 ATATGTGTCACATCATTATTTTAT
1 ACATGTGTCACATCATTATTTTAT
2595729 ACATGTG
1 ACATGTG
2595736 ACATAAGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (24 bp):
ACATGTGTCACATCATTATTTTAT
Found at i:2596724 original size:29 final size:29
Alignment explanation
Indices: 2596692--2596752 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
2596682 ATTGAACCAA
*
2596692 AATTTATTTGAAAATTATTAACAAAACCG
1 AATTAATTTGAAAATTATTAACAAAACCG
**
2596721 AATTAATTTGAAAATTATTAACTGAACCG
1 AATTAATTTGAAAATTATTAACAAAACCG
2596750 AAT
1 AAT
2596753 AAACCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACAAAACCG
Found at i:2596802 original size:135 final size:136
Alignment explanation
Indices: 2596654--2596952 Score: 357
Period size: 135 Copynumber: 2.2 Consensus size: 136
2596644 CGGTTAAGGA
* * *** ** *
2596654 AAAAAATTTGGTTAATTTTGTTTGGTTAATTGAACCAAAATTTATTTGAAAATTATTAACAAAAC
1 AAAAAATTCGGTTAATTTGGTTCAATTAATCAAACCAAAATTTATTTGAAAAATATTAACAAAAC
* **
2596719 CGAATTAATTTGAAAATTATTAACTGAACCGAATAAACC-AAATTTTTAAAAAATTATGAATTAA
66 CAAATTAATTTGAAAATTATTAACCAAACCGAATAAACCGAAATTTTTAAAAAATTATGAATTAA
2596783 TTGAAG
131 TTGAAG
*
2596789 AAAAAATTCGGTTAATTTGGTTCAATTAATCAAACCAAAATTTATTTGAAAAATATTAACCAAAC
1 AAAAAATTCGGTTAATTTGGTTCAATTAATCAAACCAAAATTTATTTGAAAAATATTAACAAAAC
* * * * *
2596854 CAAATTTATTTGAAAATTATTAACCAAACCGAATTAACCGATATTTTTTGAAAATTATTAACCGA
66 CAAATTAATTTGAAAATTATTAACCAAACCGAATAAACCGA-AATTTTT-AAAA-AATT-A-TGA
*
2596919 ATTAATCGAAG
126 ATTAATTGAAG
* * *
2596930 CAAAATTTCGGTTAATTCGGTTC
1 AAAAAATTCGGTTAATTTGGTTC
2596953 GGTTAATTTG
Statistics
Matches: 137, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
135 90 0.66
136 1 0.01
137 6 0.04
138 4 0.03
139 3 0.02
140 1 0.01
141 32 0.23
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (136 bp):
AAAAAATTCGGTTAATTTGGTTCAATTAATCAAACCAAAATTTATTTGAAAAATATTAACAAAAC
CAAATTAATTTGAAAATTATTAACCAAACCGAATAAACCGAAATTTTTAAAAAATTATGAATTAA
TTGAAG
Found at i:2596858 original size:29 final size:29
Alignment explanation
Indices: 2596813--2596888 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
2596803 ATTTGGTTCA
*
2596813 ATTAATCAAACCAAAATTTATTTGAAAAAT
1 ATTAACCAAACC-AAATTTATTTGAAAAAT
*
2596843 ATTAACCAAACCAAATTTATTTGAAAATT
1 ATTAACCAAACCAAATTTATTTGAAAAAT
*
2596872 ATTAACCAAACCGAATT
1 ATTAACCAAACCAAATT
2596889 AACCGATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
29 32 0.74
30 11 0.26
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.32
Consensus pattern (29 bp):
ATTAACCAAACCAAATTTATTTGAAAAAT
Found at i:2597101 original size:30 final size:29
Alignment explanation
Indices: 2597065--2597127 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
2597055 TTCAGTTCGG
*
2597065 TTAATCGAGATAAAATTTATTTGAAAATTA
1 TTAATCGA-ATAAAATTAATTTGAAAATTA
**
2597095 TTAATCGAATTGAATTAATTTGAAAATTA
1 TTAATCGAATAAAATTAATTTGAAAATTA
2597124 TTAA
1 TTAA
2597128 CCAAACCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (29 bp):
TTAATCGAATAAAATTAATTTGAAAATTA
Found at i:2597138 original size:29 final size:29
Alignment explanation
Indices: 2597078--2597141 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2597068 ATCGAGATAA
* * * **
2597078 AATTTATTTGAAAATTATTAATCGAATTG
1 AATTAATTTGAAAATTATTAACCAAACCG
2597107 AATTAATTTGAAAATTATTAACCAAACCG
1 AATTAATTTGAAAATTATTAACCAAACCG
2597136 AATTAA
1 AATTAA
2597142 CCGAATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCAAACCG
Found at i:2600235 original size:15 final size:16
Alignment explanation
Indices: 2600217--2600246 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2600207 AGCTCCCCCT
2600217 TTTTCATTG-AGAAAA
1 TTTTCATTGAAGAAAA
2600232 TTTTCATTGAAGAAA
1 TTTTCATTGAAGAAA
2600247 TTAAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (16 bp):
TTTTCATTGAAGAAAA
Found at i:2600656 original size:21 final size:21
Alignment explanation
Indices: 2600632--2600711 Score: 142
Period size: 21 Copynumber: 3.8 Consensus size: 21
2600622 ACTGGGGTAT
2600632 CGATACCCTGCTACAGTGTAC
1 CGATACCCTGCTACAGTGTAC
2600653 CGATACCCTGCTACAGTGTAC
1 CGATACCCTGCTACAGTGTAC
*
2600674 CGATACCCTACTACAGTGTAC
1 CGATACCCTGCTACAGTGTAC
*
2600695 CGATATCCTGCTACAGT
1 CGATACCCTGCTACAGT
2600712 AATTTCGGCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (21 bp):
CGATACCCTGCTACAGTGTAC
Found at i:2601033 original size:3 final size:3
Alignment explanation
Indices: 2601025--2601050 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2601015 GGCATAAAAT
2601025 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2601051 GCATCTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2610618 original size:24 final size:24
Alignment explanation
Indices: 2610591--2610697 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
2610581 AAACGGAGAT
*
2610591 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
2610615 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
2610639 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
2610663 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
2610687 ATCAGAAATCA
1 ATCAGAAATCA
2610698 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:2610697 original size:48 final size:48
Alignment explanation
Indices: 2610591--2610699 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
2610581 AAACGGAGAT
* * * *
2610591 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
2610639 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
2610687 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2610700 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:2611836 original size:18 final size:18
Alignment explanation
Indices: 2611810--2611886 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
2611800 ACCGGTCACA
2611810 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2611828 ACCCAACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
2611845 ----TACCCGACCCGTTA
1 ACCCGACCCGACCCGTTG
2611859 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2611877 ACCCGACCCG
1 ACCCGACCCG
2611887 TTGACCGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 12 0.24
18 38 0.76
ACGTcount: A:0.19, C:0.51, G:0.18, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2611853 original size:31 final size:31
Alignment explanation
Indices: 2611814--2611892 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
2611804 GTCACAACCC
2611814 GACCCGACCCGTTGACCCAACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
* * *
2611845 TACCCGACCCGTTAACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
2611876 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
2611893 GTTGACCCGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCAACCCGACCCGTT
Found at i:2611879 original size:8 final size:8
Alignment explanation
Indices: 2611868--2611914 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
2611858 AACCCGACCC
2611868 GACCCGTT
1 GACCCGTT
2611876 GACCC---
1 GACCCGTT
2611881 GACCCGTT
1 GACCCGTT
2611889 GA-CCGTT
1 GACCCGTT
2611896 GACCCGTT
1 GACCCGTT
2611904 GA-CCGTT
1 GACCCGTT
2611911 GACC
1 GACC
2611915 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:2611879 original size:13 final size:13
Alignment explanation
Indices: 2611833--2611907 Score: 69
Period size: 13 Copynumber: 5.2 Consensus size: 13
2611823 CGTTGACCCA
*
2611833 ACCCGACCCGTTT
1 ACCCGACCCGTTG
2611846 ACCCGACCCGTTAACCCG
1 ACCCGACCCGTT-----G
2611864 ACCCGACCCGTTG
1 ACCCGACCCGTTG
2611877 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
2611890 ACCGTTGACCCGTTG
1 ACC--CGACCCGTTG
2611905 ACC
1 ACC
2611908 GTTGACCGGA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
13 29 0.55
15 12 0.23
18 12 0.23
ACGTcount: A:0.17, C:0.45, G:0.20, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:2611896 original size:7 final size:7
Alignment explanation
Indices: 2611884--2611915 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2611874 TTGACCCGAC
2611884 CCGTTGA
1 CCGTTGA
2611891 CCGTTGA
1 CCGTTGA
2611898 CCCGTTGA
1 -CCGTTGA
2611906 CCGTTGA
1 CCGTTGA
2611913 CCG
1 CCG
2611916 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:2611901 original size:15 final size:15
Alignment explanation
Indices: 2611868--2611914 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
2611858 AACCCGACCC
*
2611868 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
2611881 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2611896 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2611911 GACC
1 GACC
2611915 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:2616788 original size:60 final size:61
Alignment explanation
Indices: 2616721--2616860 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 61
2616711 TTAAATATTC
* * *
2616721 TAATTTCATCTCTAAACTGTGAATATCGTTTTAAATTGATCATCAAACTTTT-GAACATTT
1 TAATTTCATCTCTAAACTATGAATATCATTCTAAATTGATCATCAAACTTTTAGAACATTT
* * * **
2616781 TAATTTCATCTCTAAACTATGACTTTCATTCTAAATTGGTTTTCAAACTTTTAGAACATTT
1 TAATTTCATCTCTAAACTATGAATATCATTCTAAATTGATCATCAAACTTTTAGAACATTT
* *
2616842 CAATTTCATCAC-AAACTAT
1 TAATTTCATCTCTAAACTAT
2616861 ACATATATAC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
60 51 0.74
61 18 0.26
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (61 bp):
TAATTTCATCTCTAAACTATGAATATCATTCTAAATTGATCATCAAACTTTTAGAACATTT
Found at i:2616797 original size:29 final size:29
Alignment explanation
Indices: 2616703--2616798 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
2616693 TAATTGGTCC
* * * *
2616703 CTAAATTTTTAAATATTCTAATTTCATCT
1 CTAAACTTTTGAACATTTTAATTTCATCT
* * * *
2616732 CTAAAC-TGTGAATATCGTTTTAAATTGATCAT
1 CTAAACTTTTG-A-A-CATTTTAATTTCATC-T
2616764 C-AAACTTTTGAACATTTTAATTTCATCT
1 CTAAACTTTTGAACATTTTAATTTCATCT
2616792 CTAAACT
1 CTAAACT
2616799 ATGACTTTCA
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
28 4 0.08
29 23 0.47
30 2 0.04
31 15 0.31
32 5 0.10
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (29 bp):
CTAAACTTTTGAACATTTTAATTTCATCT
Found at i:2617153 original size:60 final size:58
Alignment explanation
Indices: 2616982--2617157 Score: 167
Period size: 60 Copynumber: 2.9 Consensus size: 58
2616972 ATTTGGATGG
* * * * *
2616982 ATTTGAGGATGAAATTAGAATATTCAAAAGTTTGGAAAGCAATTTAGAAA-GAGGGTCAT
1 ATTTAAGGATAAAATTAGAATATTCAAAAGTTT-AAAACCAATTTA-AAATGAGAGTCAT
* * * **
2617041 AGTTTAGGGATAAAATTAGAA-AGTTCAAAAGCTTAAAGACTAATTTTGAATGAGAGTCATT
1 A-TTTAAGGATAAAATTAGAATA-TTCAAAAGTTTAAA-ACCAATTTAAAATGAGAGTCA-T
* *
2617102 ATTTAAGGATAAAATTAGAATATTTAAAAGTTTAATAACCAGTTTAAAATGAGAGT
1 ATTTAAGGATAAAATTAGAATATTCAAAAGTTTAA-AACCAATTTAAAATGAGAGT
2617158 TATAATTTGG
Statistics
Matches: 93, Mismatches: 17, Indels: 13
0.76 0.14 0.11
Matches are distributed among these distances:
59 6 0.06
60 83 0.89
61 4 0.04
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.31
Consensus pattern (58 bp):
ATTTAAGGATAAAATTAGAATATTCAAAAGTTTAAAACCAATTTAAAATGAGAGTCAT
Found at i:2619193 original size:14 final size:15
Alignment explanation
Indices: 2619176--2619204 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2619166 TTATACTATT
2619176 TATTG-TATAAATAA
1 TATTGATATAAATAA
2619190 TATTGATATAAATAA
1 TATTGATATAAATAA
2619205 CATTAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TATTGATATAAATAA
Found at i:2620415 original size:95 final size:96
Alignment explanation
Indices: 2620243--2620433 Score: 260
Period size: 95 Copynumber: 2.0 Consensus size: 96
2620233 AGATTATAAT
* ** *
2620243 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTAATTAAACGTTCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTAATTAAACGCCCCGACTTTA
* * *
2620308 TGAATAATATTCAGCTAGCTTGATAAAGGTG
66 TGAATAAGATTCAACTAACTTGATAAAGGTG
* * **
2620339 ATTATAT-TATACAATAAAGCTTGAGTTTTCTCTCTAAAGCAATTGGTTAAACGCCCCGACTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTAATTAAACGCCCCGACTTTA
2620403 T-AGATAAGATTCAACTAACTTGATAAAGGTG
66 TGA-ATAAGATTCAACTAACTTGATAAAGGTG
2620434 TTTACGTATT
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
94 1 0.01
95 75 0.90
96 7 0.08
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (96 bp):
ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTAATTAAACGCCCCGACTTTA
TGAATAAGATTCAACTAACTTGATAAAGGTG
Found at i:2621678 original size:36 final size:36
Alignment explanation
Indices: 2621568--2621685 Score: 112
Period size: 36 Copynumber: 3.3 Consensus size: 36
2621558 TAATGCAGAT
*
2621568 GATTTATCTCACTTGAGATTGATTTTCTTAAAAC-A
1 GATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * * * *** *
2621603 GACTTTGTCTCACTTGGGACTGTTTTACCCGAAATAA
1 GA-TTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* *
2621640 GATTTATTTCACTTAAGATTGTTTTTCTTAAAACAA
1 GATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
*
2621676 GATTTGTCTC
1 GATTTATCTC
2621686 GCTTAAGACC
Statistics
Matches: 60, Mismatches: 21, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
35 2 0.03
36 55 0.92
37 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (36 bp):
GATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:2621861 original size:37 final size:38
Alignment explanation
Indices: 2621728--2621880 Score: 166
Period size: 39 Copynumber: 4.0 Consensus size: 38
2621718 GTTTTTAAAG
* *
2621728 AAGATTTTATATCACTTGAGATAGTTTCCCTCGAAACA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACA
* *
2621766 GAAGATTTTCTCAT-GCTTGAGATAGTTTCCCTCGAGACAA
1 -AAGATTTTATC-TCGCTTGAGATAGTTTCCCTCGAAAC-A
**
2621806 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTAAAACA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACA
* * * * *
2621844 AA-ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACA
2621881 TAAACATTGA
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
37 30 0.31
38 4 0.04
39 62 0.63
40 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (38 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACA
Found at i:2621943 original size:36 final size:36
Alignment explanation
Indices: 2621896--2621981 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
2621886 ATTGAAAACA
* ** * * *
2621896 TTTCCATTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTCAGACAG
2621932 TTTCCCTTGAAACAAATTTTGTCTCCCTTCAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTCAGACAG
*
2621968 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2621982 TAAACTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTCAGACAG
Found at i:2621985 original size:101 final size:102
Alignment explanation
Indices: 2621809--2622008 Score: 321
Period size: 101 Copynumber: 2.0 Consensus size: 102
2621799 GAGACAAAAG
*
2621809 ATTTTATCTCGCTTGAGATAGTTTCCCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTAAAACAAAATTTTGTCTCCCTTCAGACAGTTTCTCT
*
2621874 TGAAACATAAACATTGAAAACATTTCCATTGAAATGA
66 TGAAACATAAACATTAAAAACATTTCCATTGAAATGA
* * *
2621911 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTCAGACAGTTTCTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTAAAACAAAATTTTGTCTCCCTTCAGACAGTTTCTCT
* * *
2621975 TGAAACATAAACTTTAAAAACGTTTCCCTTGAAA
66 TGAAACATAAACATTAAAAACATTTCCATTGAAA
2622009 CACAAAATAT
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 59 0.66
102 31 0.34
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (102 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTTAAAACAAAATTTTGTCTCCCTTCAGACAGTTTCTCT
TGAAACATAAACATTAAAAACATTTCCATTGAAATGA
Found at i:2622155 original size:30 final size:30
Alignment explanation
Indices: 2622119--2622194 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
2622109 CTCTTGACAC
2622119 AGTTTCTCTTGAAACACCAACCTTTGAGAT
1 AGTTTCTCTTGAAACACCAACCTTTGAGAT
2622149 AGTTTCTCTTGAAACACCAACCTTTGAGAT
1 AGTTTCTCTTGAAACACCAACCTTTGAGAT
* *
2622179 TGTTTCACTTGAAACA
1 AGTTTCTCTTGAAACA
2622195 AATTTCTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.34
Consensus pattern (30 bp):
AGTTTCTCTTGAAACACCAACCTTTGAGAT
Found at i:2622211 original size:96 final size:97
Alignment explanation
Indices: 2622045--2622231 Score: 225
Period size: 96 Copynumber: 1.9 Consensus size: 97
2622035 TGAAACGAGT
** * * **
2622045 TTTGAGACAATTTCCCTTGAAACACCCGCATTTGATATTGTTTCCCTTGAAACATGTTTTGTCTC
1 TTTGAGACAATTTCCCTTGAAACACCAACATTTGAGATTGTTTCACTTGAAACAAATTTTGTCTC
* *
2622110 TCTTGACAC-AGTTTCTCTTGAAACACCAACC
66 GCTTGACACAAGTTTCCCTTGAAACACCAACC
* * * *
2622141 TTTGAGATAGTTTCTCTTGAAACACCAACCTTTGAGATTGTTTCACTTGAAACAAATTTCT-TCT
1 TTTGAGACAATTTCCCTTGAAACACCAACATTTGAGATTGTTTCACTTGAAACAAATTT-TGTCT
* *
2622205 CGCTTGAGACAATTTTCCCTTGAAACA
65 CGCTTGACACAAGTTTCCCTTGAAACA
2622232 AGAAATTTTA
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
96 60 0.80
97 15 0.20
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (97 bp):
TTTGAGACAATTTCCCTTGAAACACCAACATTTGAGATTGTTTCACTTGAAACAAATTTTGTCTC
GCTTGACACAAGTTTCCCTTGAAACACCAACC
Found at i:2623875 original size:2 final size:2
Alignment explanation
Indices: 2623862--2623954 Score: 177
Period size: 2 Copynumber: 46.5 Consensus size: 2
2623852 CCCTTGTATG
*
2623862 TA TA TG TA TA 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
2623904 TA TA TA TA TA 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
2623946 TA TA TA TA T
1 TA TA TA TA T
2623955 TTTAATTATA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2624044 original size:3 final size:3
Alignment explanation
Indices: 2624038--2624216 Score: 80
Period size: 3 Copynumber: 62.0 Consensus size: 3
2624028 ACGTAAAAAA
*
2624038 ATT ATT ATT -TT -TT ATAT ATT -TAT ATT -TT -TT ATT -TT ATT CCTT
1 ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT -ATT
* * *
2624080 ATT ATT ATT -TT ATT -TT CTT TTT AGT ATT ATT ATT ATT ATAT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T
* * *
2624125 ATT ATTT ATT -TT ATT -TT A-T ACT CTT -TT ACT ATT -TT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * ** *
2624166 ATT -TCT ATT TTT CTT ATT ATT TTT ATT ATT CCT AGT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2624211 ATT ATT
1 ATT ATT
2624217 TTTACCTTTA
Statistics
Matches: 138, Mismatches: 20, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
2 26 0.19
3 95 0.69
4 17 0.12
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2624184 original size:70 final size:70
Alignment explanation
Indices: 2624038--2624186 Score: 169
Period size: 70 Copynumber: 2.1 Consensus size: 70
2624028 ACGTAAAAAA
* * * * * *
2624038 ATTATTATTTTTTATATATTTATATTTTTTATTTTATTCCTTATTATTATTTTATTTTCTTTTTA
1 ATTATTATTATATATATATTTATATTTTTTATTTTATACCTTATTACTATTTTATTTTATTTCTA
2624103 GTATT
66 GTATT
2624108 ATTATTATTATATATATA-TTAT-TTATTTTATTTTATACTCTT-TTACTATTTTATTATTATTT
1 ATTATTATTATATATATATTTATATT-TTTTATTTTATAC-CTTATTACTATTTTATT-TTATTT
* *
2624170 CTATTTTT
63 CTAGTATT
*
2624178 CTTATTATT
1 ATTATTATT
2624187 TTTATTATTC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
68 2 0.03
69 28 0.42
70 37 0.55
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.69
Consensus pattern (70 bp):
ATTATTATTATATATATATTTATATTTTTTATTTTATACCTTATTACTATTTTATTTTATTTCTA
GTATT
Found at i:2624232 original size:2 final size:2
Alignment explanation
Indices: 2624225--2624253 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2624215 TTTTTACCTT
2624225 TA 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 TA T
2624254 TATGTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2624422 original size:16 final size:16
Alignment explanation
Indices: 2624400--2624441 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2624390 TATTTTTCTG
*
2624400 GTGTTTTGTT-TTCCT
1 GTGTTTTTTTATTCCT
*
2624415 GTGTTTTTTTATTCTT
1 GTGTTTTTTTATTCCT
2624431 GTGTTATTTTT
1 GTGTT-TTTTT
2624442 TTGCCTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 9 0.39
17 5 0.22
ACGTcount: A:0.05, C:0.07, G:0.17, T:0.71
Consensus pattern (16 bp):
GTGTTTTTTTATTCCT
Found at i:2628740 original size:95 final size:95
Alignment explanation
Indices: 2628576--2628763 Score: 288
Period size: 95 Copynumber: 2.0 Consensus size: 95
2628566 ATATTACATA
* * * *
2628576 TATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGACTTTATGGATAAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAAATGGTTAAACGCCTCGACTTTATGGATAAG
*
2628641 ATTCAACTAGCCTGATAAAGGTGATTATAC
66 ATTCAACTAACCTGATAAAGGTGATTATAC
*
2628671 TATACAATAAAGCTTGAGTTGTTCCTCTAAAGCAAATGGTTAAACGACCT-GACTTTATGGATAA
1 TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAAATGGTTAAACG-CCTCGACTTTATGGATAA
* *
2628735 GATTCAGCTAACCTGATAAAGGTGTTTAT
65 GATTCAACTAACCTGATAAAGGTGATTAT
2628764 GTATTAAGTT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 81 0.96
96 3 0.04
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAAATGGTTAAACGCCTCGACTTTATGGATAAG
ATTCAACTAACCTGATAAAGGTGATTATAC
Found at i:2630204 original size:37 final size:39
Alignment explanation
Indices: 2630069--2630223 Score: 197
Period size: 39 Copynumber: 4.0 Consensus size: 39
2630059 CTGTTTTTAA
2630069 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
2630108 AGAAGATTTTGTCTCTCTTGAGATAGTTTCCCTCGAGAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
2630147 AAAATATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
2630186 A-AA-ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
2630223 A
1 A
2630224 TAAATATTGA
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
37 31 0.30
38 2 0.02
39 70 0.68
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:2630286 original size:36 final size:36
Alignment explanation
Indices: 2630239--2630322 Score: 123
Period size: 36 Copynumber: 2.3 Consensus size: 36
2630229 ATTGAAAACA
* * * *
2630239 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTTATCTCCCTTGAGACAG
2630275 TTTCCCTTGAAATAAATTTTATCTCCCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTATCTCCCTTGAGACAG
*
2630311 TTTCTCTTGAAA
1 TTTCCCTTGAAA
2630323 CATAAACTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTATCTCCCTTGAGACAG
Found at i:2630328 original size:101 final size:102
Alignment explanation
Indices: 2630152--2630351 Score: 323
Period size: 101 Copynumber: 2.0 Consensus size: 102
2630142 GAGACAAAAT
*
2630152 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCT
2630217 TGAAACATAAA-TATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACT-TTGAAAACATTTCCCTTGAAATGA
* * *
2630254 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA-TAAATTTTATCTCCCTTGAGACAGTTTCTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCT
* *
2630318 TGAAACATAAACTTTGAAAACGTTTCCTTTGAAA
66 TGAAACATAAACTTTGAAAACATTTCCCTTGAAA
2630352 CACAAAATAT
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
101 59 0.65
102 32 0.35
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (102 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACTTTGAAAACATTTCCCTTGAAATGA
Found at i:2630496 original size:30 final size:30
Alignment explanation
Indices: 2630455--2630537 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
2630445 TTTGTCTCTC
* *
2630455 TTGAGACAGTTTCTCTTTAAACACCAACCT
1 TTGAGATAGTTTCTCTTGAAACACCAACCT
*
2630485 TTGAGATAGTTTCTCTTGAAACATCAACCT
1 TTGAGATAGTTTCTCTTGAAACACCAACCT
* *
2630515 TTGAGATTGTTTCCCTTGAAACA
1 TTGAGATAGTTTCTCTTGAAACA
2630538 AATTTCGTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (30 bp):
TTGAGATAGTTTCTCTTGAAACACCAACCT
Found at i:2630543 original size:16 final size:17
Alignment explanation
Indices: 2630524--2630575 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
2630514 TTTGAGATTG
2630524 TTTCCCTTGAAACAAAT
1 TTTCCCTTGAAACAAAT
*
2630541 TTCGTCTCGCTTGAGAC-AAT
1 TT--TC-C-CTTGAAACAAAT
2630561 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
2630576 GAAATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
16 7 0.25
17 4 0.14
18 2 0.07
19 2 0.07
20 6 0.21
21 7 0.25
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.35
Consensus pattern (17 bp):
TTTCCCTTGAAACAAAT
Found at i:2632355 original size:27 final size:29
Alignment explanation
Indices: 2632325--2632397 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
2632315 TAACATTTTT
*
2632325 TTATATTTTTTATTTTA-T-TCCTTATTA
1 TTATATTTTTTATTTTAGTATCATTATTA
*
2632352 TTATTATTTTTCT-TTTTAGTATTATTATTA
1 TTA-TATTTTT-TATTTTAGTATCATTATTA
2632382 TATATATTTTTTATTT
1 T-TATATTTTTTATTT
2632398 CGCTTTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 3 0.08
28 12 0.32
29 3 0.08
30 18 0.47
31 2 0.05
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.71
Consensus pattern (29 bp):
TTATATTTTTTATTTTAGTATCATTATTA
Found at i:2632391 original size:24 final size:24
Alignment explanation
Indices: 2632347--2632392 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2632337 TTTTATTCCT
* * *
2632347 TATTATTATTATTTTTCTTTTTAG
1 TATTATTATTATATATATTTTTAG
2632371 TATTATTATTATATATATTTTT
1 TATTATTATTATATATATTTTT
2632393 TATTTCGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (24 bp):
TATTATTATTATATATATTTTTAG
Found at i:2632501 original size:2 final size:2
Alignment explanation
Indices: 2632494--2632526 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2632484 CCTATTTTTG
2632494 TA TA TA 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 TA TA TA T
2632527 GTTTTATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2632700 original size:31 final size:29
Alignment explanation
Indices: 2632657--2632734 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
2632647 TATACTATTT
*
2632657 TCTTTTTGTTATTTTTATGGTAATTTTTCTG
1 TCTTTTTTTTATTTTTAT-GTAATTTTT-TG
* * * *
2632688 TGTTTTTTTTATTCTAATGTTATTTTTTG
1 TCTTTTTTTTATTTTTATGTAATTTTTTG
*
2632717 TCTTATTTTTATTTTTAT
1 TCTTTTTTTTATTTTTAT
2632735 ATTTATTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 16 0.42
30 8 0.21
31 14 0.37
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.72
Consensus pattern (29 bp):
TCTTTTTTTTATTTTTATGTAATTTTTTG
Found at i:2634515 original size:2 final size:2
Alignment explanation
Indices: 2634508--2634554 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2634498 CTATTCAATG
2634508 TA TA TA TA TA 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
2634550 TA TA T
1 TA TA T
2634555 GTGGAGAAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2636153 original size:7 final size:7
Alignment explanation
Indices: 2636141--2636169 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2636131 GTTTTAGACA
2636141 TGCTGGT
1 TGCTGGT
2636148 TGCTGGT
1 TGCTGGT
2636155 TGCTGGT
1 TGCTGGT
2636162 TGCTGGT
1 TGCTGGT
2636169 T
1 T
2636170 AGGTTTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.41, T:0.45
Consensus pattern (7 bp):
TGCTGGT
Found at i:2637816 original size:26 final size:25
Alignment explanation
Indices: 2637785--2637835 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
2637775 TTTTAGTCTC
*
2637785 TTAAAATTTTAAAAGTTTATCTCTTT
1 TTAAAATTTTAAAACTTTA-CTCTTT
2637811 TTAAAATTTTAAAACTTTACTCTTT
1 TTAAAATTTTAAAACTTTACTCTTT
2637836 AATATAAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (25 bp):
TTAAAATTTTAAAACTTTACTCTTT
Found at i:2638685 original size:18 final size:18
Alignment explanation
Indices: 2638662--2638699 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2638652 GTTAACGATA
*
2638662 AGGCTTAGTTGCCTAAGG
1 AGGCTTAGTTGCCCAAGG
2638680 AGGCTTAGTTGCCCAAGG
1 AGGCTTAGTTGCCCAAGG
2638698 AG
1 AG
2638700 TGCTACTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (18 bp):
AGGCTTAGTTGCCCAAGG
Found at i:2640993 original size:18 final size:19
Alignment explanation
Indices: 2640970--2641012 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2640960 TCAGTAATCC
2640970 TATTCT-CTGGTAATCTTA
1 TATTCTACTGGTAATCTTA
2640988 TATTCTCACTGGTAATCTTA
1 TATTCT-ACTGGTAATCTTA
*
2641008 CATTC
1 TATTC
2641013 GGTGAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (19 bp):
TATTCTACTGGTAATCTTA
Found at i:2649741 original size:2 final size:2
Alignment explanation
Indices: 2649734--2649771 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2649724 AATAAGGGAA
2649734 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
2649772 GATCCCTGAC
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:2650045 original size:41 final size:41
Alignment explanation
Indices: 2649998--2650180 Score: 287
Period size: 41 Copynumber: 4.5 Consensus size: 41
2649988 ATTCGCGATG
* * ** *
2649998 CATTTCGCGTTGCGATAGT-TGAAAATCACGTTGCGGTTTTC
1 CATTTCGCGTTGCGATAGTCT-ACAGTGTCGTTGCGATTTTC
*
2650039 TATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
*
2650080 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGGTTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
2650121 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
2650162 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
2650181 TTTAAAAATA
Statistics
Matches: 132, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
41 131 0.99
42 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
Found at i:2650060 original size:20 final size:20
Alignment explanation
Indices: 2650037--2650180 Score: 69
Period size: 20 Copynumber: 7.0 Consensus size: 20
2650027 GTTGCGGTTT
2650037 TCTATTTCGCGTTGCGATAG
1 TCTATTTCGCGTTGCGATAG
** **
2650057 TCTACAGT-GTCGTTGCGATTT
1 TCTA-TTTCG-CGTTGCGATAG
*
2650078 TCCATTTCGCGTTGCGATAG
1 TCTATTTCGCGTTGCGATAG
** * **
2650098 TCTACAGT-GTCGTTGCGGTTT
1 TCTA-TTTCG-CGTTGCGATAG
*
2650119 TCCATTTCGCGTTGCGATAG
1 TCTATTTCGCGTTGCGATAG
** **
2650139 TCTACAGT-GTCGTTGCGATTT
1 TCTA-TTTCG-CGTTGCGATAG
*
2650160 TCCATTTCGCGTTGCGATAG
1 TCTATTTCGCGTTGCGATAG
2650180 T
1 T
2650181 TTTAAAAATA
Statistics
Matches: 84, Mismatches: 31, Indels: 18
0.63 0.23 0.14
Matches are distributed among these distances:
20 43 0.51
21 41 0.49
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.40
Consensus pattern (20 bp):
TCTATTTCGCGTTGCGATAG
Found at i:2650072 original size:21 final size:21
Alignment explanation
Indices: 2650046--2650157 Score: 83
Period size: 21 Copynumber: 5.4 Consensus size: 21
2650036 TTCTATTTCG
2650046 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
2650067 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
2650085 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* * * *
2650108 CGTTGCGGT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
2650126 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
2650149 CGTTGCGAT
1 CGTTGCGAT
2650158 TTTCCATTTC
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
18 4 0.06
19 8 0.12
20 17 0.25
21 26 0.39
22 8 0.12
23 4 0.06
ACGTcount: A:0.14, C:0.21, G:0.27, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:2651001 original size:5 final size:5
Alignment explanation
Indices: 2650991--2651017 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2650981 CCGCCGCCGC
2650991 CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CG
2651018 GGTAGTGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:2661101 original size:66 final size:66
Alignment explanation
Indices: 2660984--2661107 Score: 158
Period size: 66 Copynumber: 1.9 Consensus size: 66
2660974 AAATTCCATA
* * * * **
2660984 AGGAATTACCAGTCGGTGCTGAACCTATAAAAGAAATTACCAATAGTGACTGAACCTGCCAGAGA
1 AGGAATTACAAGTAGGTGCTGAACCAATAAAAGAAATTACCAACAACGACTGAACCTGCCAGAGA
2661049 T
66 T
* * **
2661050 AGGAATTACAAGTAGGTGCTGAACCAATACAAGGAATTACCCGCAACGACTGAACCTG
1 AGGAATTACAAGTAGGTGCTGAACCAATAAAAGAAATTACCAACAACGACTGAACCTG
2661108 TTAGAGTCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 48 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (66 bp):
AGGAATTACAAGTAGGTGCTGAACCAATAAAAGAAATTACCAACAACGACTGAACCTGCCAGAGA
T
Found at i:2661214 original size:24 final size:24
Alignment explanation
Indices: 2661174--2661221 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2661164 ACAGATACAT
* *
2661174 CAGAAATCAGAGCAGAAATCAGAG
1 CAGAAATCAGAACAGAAATAAGAG
*
2661198 CAGAAATCAGAATAGAAATAAGAG
1 CAGAAATCAGAACAGAAATAAGAG
2661222 AAAACATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.12, G:0.23, T:0.10
Consensus pattern (24 bp):
CAGAAATCAGAACAGAAATAAGAG
Found at i:2661216 original size:12 final size:12
Alignment explanation
Indices: 2661174--2661208 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
2661164 ACAGATACAT
2661174 CAGAAATCAGAG
1 CAGAAATCAGAG
2661186 CAGAAATCAGAG
1 CAGAAATCAGAG
2661198 CAGAAATCAGA
1 CAGAAATCAGA
2661209 ATAGAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.17, G:0.23, T:0.09
Consensus pattern (12 bp):
CAGAAATCAGAG
Found at i:2661558 original size:20 final size:20
Alignment explanation
Indices: 2661518--2661563 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2661508 ATGCAAAATG
* *
2661518 AGTATCGATACTGGTATAGT
1 AGTATCGATACTGCTACAGT
2661538 AGTATCGATACTGCTACAGT
1 AGTATCGATACTGCTACAGT
*
2661558 AATATC
1 AGTATC
2661564 AAGCCCAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTGCTACAGT
Found at i:2666674 original size:22 final size:24
Alignment explanation
Indices: 2666625--2666675 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
2666615 TAAGTCGAAG
*
2666625 TCAACAGTCAACTGGTTGACTCGG
1 TCAACAGTCAACTGGTTGACTCGA
2666649 TCAA-AGTCAAC-GGTTTGAC-CGA
1 TCAACAGTCAACTGG-TTGACTCGA
2666671 TCAAC
1 TCAAC
2666676 GGTTTGGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 8 0.33
23 12 0.50
24 4 0.17
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (24 bp):
TCAACAGTCAACTGGTTGACTCGA
Found at i:2671378 original size:31 final size:31
Alignment explanation
Indices: 2671343--2671439 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
2671333 ATAAATAAAT
* * *
2671343 TTTAACCCCTGAATTTTAGATAAAACATTAA
1 TTTAACCCCTAAATTTTATATAAAATATTAA
***
2671374 TTTAA-TTTTAAA-TTTATATAAAAGTATTAA
1 TTTAACCCCTAAATTTTATATAAAA-TATTAA
2671404 TTTAACCCCTAAATTTTATATAAAATATTAA
1 TTTAACCCCTAAATTTTATATAAAATATTAA
2671435 TTTAA
1 TTTAA
2671440 TATTAAATCC
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
29 10 0.19
30 13 0.24
31 20 0.37
32 11 0.20
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (31 bp):
TTTAACCCCTAAATTTTATATAAAATATTAA
Found at i:2671388 original size:30 final size:30
Alignment explanation
Indices: 2671354--2671447 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
2671344 TTAACCCCTG
* * *
2671354 AATTTTAGATAAAACATTAATTTAATTTTA
1 AATTTTATATAAAATATTAATTTAATATTA
***
2671384 AA-TTTATATAAAAGTATTAATTTAACCCCTA
1 AATTTTATATAAAA-TATTAATTTAA-TATTA
2671415 AATTTTATATAAAATATTAATTTAATATTA
1 AATTTTATATAAAATATTAATTTAATATTA
2671445 AAT
1 AAT
2671448 CCAGTCAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
29 10 0.19
30 17 0.32
31 15 0.28
32 11 0.21
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (30 bp):
AATTTTATATAAAATATTAATTTAATATTA
Found at i:2671880 original size:2 final size:2
Alignment explanation
Indices: 2671873--2671914 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2671863 AACACATGAT
2671873 TA TA TA TA TA 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
2671915 ATTTTAATGA
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):
TA
Found at i:2676319 original size:3 final size:3
Alignment explanation
Indices: 2676311--2676429 Score: 202
Period size: 3 Copynumber: 39.7 Consensus size: 3
2676301 TTTTTATCCA
*
2676311 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2676359 TAC TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2676407 TAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
2676430 AATATATTAA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2676469 original size:20 final size:19
Alignment explanation
Indices: 2676428--2676472 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2676418 CTATTATTAT
* *
2676428 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
2676447 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
2676467 TAAATA
1 TAAATA
2676473 ATAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:2689306 original size:16 final size:17
Alignment explanation
Indices: 2689285--2689317 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2689275 ATGCTTGAAG
2689285 AAAG-AAAAGAAAAAAA
1 AAAGAAAAAGAAAAAAA
2689301 AAAGAAAAAGAAAAAAA
1 AAAGAAAAAGAAAAAAA
2689318 GGGGGGGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAAA
Found at i:2690583 original size:83 final size:82
Alignment explanation
Indices: 2690394--2690851 Score: 749
Period size: 83 Copynumber: 5.5 Consensus size: 82
2690384 TAATGTGCTC
* *
2690394 AATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTGAACATAACCAATCATTGAAC
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACATAACCAATCATTGAAT
2690459 TAGAAGATGAATTTGTT
66 TAGAAGATGAATTTGTT
2690476 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACATAACCAATCATTGAAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACATAACCAATCATTGAA-
2690541 TTAGAAGATGAATTTGTT
65 TTAGAAGATGAATTTGTT
* *
2690559 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-GCAGAACCAATCATTGAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGAACATAACCAATCATTGAA
2690623 GTTAGAAGATGAATTTGTT
65 -TTAGAAGATGAATTTGTT
*
2690642 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACATAACCAATCATTGAAC
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACATAACCAATCATTGAAT
2690707 TAGAAGATGAATTTGTT
66 TAGAAGATGAATTTGTT
* *
2690724 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-GCAGAACCAATCATTGAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGAACATAACCAATCATTGAA
* **
2690788 TTTAGAAGATGAATGTGCCC
65 -TTAGAAGATGAATTTG-TT
*
2690808 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
2690852 TGGCAGAACT
Statistics
Matches: 356, Mismatches: 14, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
82 141 0.40
83 171 0.48
84 44 0.12
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (82 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACATAACCAATCATTGAAT
TAGAAGATGAATTTGTT
Found at i:2690713 original size:165 final size:165
Alignment explanation
Indices: 2690394--2690851 Score: 785
Period size: 165 Copynumber: 2.8 Consensus size: 165
2690384 TAATGTGCTC
* * *
2690394 AATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGG-TTGAACATAACCAATCATTGAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-GCAGAACCAATCATTGAA
*
2690458 CTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAA
65 TTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAA
*
2690523 CATAACCAATCATTGAAGTTAGAAGATGAATTTGTT
130 CATAACCAATCATTGAAGCTAGAAGATGAATTTGTT
2690559 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA-
2690624 TTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAA
65 TTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAA
2690689 CATAACCAATCATTGAA-CTAGAAGATGAATTTGTT
130 CATAACCAATCATTGAAGCTAGAAGATGAATTTGTT
2690724 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA-
* ** *
2690789 TTAGAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTT
65 TTAGAAGATGAATTTG-TTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
2690852 TGGCAGAACT
Statistics
Matches: 280, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
165 153 0.55
166 127 0.45
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (165 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
TAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAAC
ATAACCAATCATTGAAGCTAGAAGATGAATTTGTT
Found at i:2691733 original size:114 final size:114
Alignment explanation
Indices: 2691533--2691791 Score: 407
Period size: 114 Copynumber: 2.3 Consensus size: 114
2691523 TGCAAGGGAA
*
2691533 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTGCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTGCATAATGAGAAGAACTTGTTC
* * * *
2691598 ACCCTTTTGTTTAAATTCATCATTTGATGGATCATTCTTTTCCAG-GTAG
66 AACCTTTTGTTTAAATTCATCACTTGATGGATCATT-TTTGCCAGAGAAG
*
2691647 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTGCATAATGAGAAGAACTTGTTC
* *
2691712 AACCTTTT-TTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAG
66 AACCTTTTGTT-TAAATTCATCACTTGATGGATCATTTTTGCCAGAGAAG
2691761 -GTTCATAATGAGAAGAACTCATCTGAAGAAG
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAG
2691792 AACTTGTTCA
Statistics
Matches: 135, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
113 40 0.30
114 95 0.70
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (114 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTGCATAATGAGAAGAACTTGTTC
AACCTTTTGTTTAAATTCATCACTTGATGGATCATTTTTGCCAGAGAAG
Found at i:2691803 original size:89 final size:90
Alignment explanation
Indices: 2691698--2691881 Score: 257
Period size: 89 Copynumber: 2.1 Consensus size: 90
2691688 GTTCATAATG
* ** **
2691698 AGAAGAACTTGTTCAACCTT-TT-TTCTGAATTCATCACTTGATGGATTATTTTTGCCAG-AGAA
1 AGAAGAACTTGTTCAA-CTTCTTGTT-TGAATTCATCACTTGATGGATCATCATCCCCAGCAGAA
*
2691760 GGTTCATAATGAGAAGAACTCATCTGA
64 AGTTCATAATGAGAAGAACTCATCTGA
*
2691787 AGAAGAACTTGTTCAACTTCTTGTTTGAATTCATCATTTGATGGATCATCATCCCCAGCAGAAAG
1 AGAAGAACTTGTTCAACTTCTTGTTTGAATTCATCACTTGATGGATCATCATCCCCAGCAGAAAG
*
2691852 TTCATAATGAGAAGAACTTATCTGA
66 TTCATAATGAGAAGAACTCATCTGA
2691877 AGAAG
1 AGAAG
2691882 GAAGAAGAAG
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
88 3 0.04
89 45 0.54
90 36 0.43
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (90 bp):
AGAAGAACTTGTTCAACTTCTTGTTTGAATTCATCACTTGATGGATCATCATCCCCAGCAGAAAG
TTCATAATGAGAAGAACTCATCTGA
Found at i:2691933 original size:203 final size:206
Alignment explanation
Indices: 2691584--2692227 Score: 677
Period size: 203 Copynumber: 3.0 Consensus size: 206
2691574 GTGCATAATG
* * * ** *
2691584 AGAAGAATTTGTTCACCCTTTTGTTTAAATTCATCATTTGATGGATCATTCTTTTCCAGGTAGAG
1 AGAAGAACTTGTTCACACTTTTGTTTAAATTCATCATTTGATGGATCATTCATCCCCAGGTAAAG
2691649 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
66 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* *
2691714 CCTTTTTTCTGAATTCATC-ACTTGATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGA
131 CCTTTTTTCTGAATTCATCAAATTGATGGATTATCTTTGCCAG-GAAGAGTTCATAATGAGAAGA
2691777 A-C-TCATCTGA
195 ACCGTCATCTGA
*
2691787 AGAAGAACTTGTTCA-ACTTCTTGTTTGAATTCATCATTTGATGGATCA-TCATCCCCAGCAG-A
1 AGAAGAACTTGTTCACACTT-TTGTTTAAATTCATCATTTGATGGATCATTCATCCCCAG--GTA
*
2691849 AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
63 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
2691914 CAACCTTTTTTCTGAATTCATCAAATTGATGGATTATCTTTGCCAGGTAGAGTTCATAATGAGAA
128 CAACCTTTTTTCTGAATTCATCAAATTGATGGATTATCTTTGCCAGGAAGAGTTCATAATGAGAA
2691979 GAACTCGTCATCTGAAGAAGGA
193 GAAC-CGTCATCT-------GA
* *
2692001 AGAAGAAGTTCATAATGAGAAGAATTTGTTCA-ACCTTTTGCTTGAATTCATCATTTGATGGATC
1 AGAAGAA---C--------------TTGTTCACA-CTTTTGTTTAAATTCATCATTTGATGGATC
* ** *
2692065 A-ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCA
48 ATTCATCCCCAGGTAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCA
* * ** *
2692129 TAATAAGAAGAATTTGTTCAACCTTTTACCTGAATTCATC-AATTGATGGATCAGTCTTT-CCAG
110 TAATGAGAAGAACTTGTTCAACCTTTTTTCTGAATTCATCAAATTGATGGATTA-TCTTTGCCAG
2692192 AGAA-AGTTCATAATGAGAAGAA-C-TCATCTGA
174 -GAAGAGTTCATAATGAGAAGAACCGTCATCTGA
2692223 AGAAG
1 AGAAG
2692228 GAAGAAGAAG
Statistics
Matches: 379, Mismatches: 23, Indels: 59
0.82 0.05 0.13
Matches are distributed among these distances:
202 10 0.03
203 130 0.34
204 39 0.10
206 1 0.00
207 6 0.02
214 9 0.02
217 1 0.00
222 7 0.02
229 7 0.02
230 20 0.05
231 42 0.11
232 38 0.10
233 69 0.18
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (206 bp):
AGAAGAACTTGTTCACACTTTTGTTTAAATTCATCATTTGATGGATCATTCATCCCCAGGTAAAG
TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTTTTCTGAATTCATCAAATTGATGGATTATCTTTGCCAGGAAGAGTTCATAATGAGAAGAA
CCGTCATCTGA
Found at i:2692121 original size:116 final size:115
Alignment explanation
Indices: 2691787--2692267 Score: 656
Period size: 116 Copynumber: 4.2 Consensus size: 115
2691777 ACTCATCTGA
* * **
2691787 AGAAGAACTTGTTCAA-CTTCTTGTTTGAATTCATCATTTGATGGATCATCATCCCCAGCAGAAA
1 AGAAGAACTTGTTCAACCTT-TTGCTTGAATTCATCAATTGATGGATCATCATTGCCAG-AGAAA
2691851 GTTCATAATGAGAAGAACT-T-ATCTGAAGAAGGAAGAAGAAGTTCATAATG
64 GTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
2691901 AGAAGAACTTGTTCAACCTTTT-TTCTGAATTCATCAAATTGATGGATTATCTTTGCCAG-GTAG
1 AGAAGAACTTGTTCAACCTTTTGCT-TGAATTCATC-AATTGATGGATCATCATTGCCAGAG-AA
2691964 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
63 AGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
2692018 AGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAATTGATGGATCATCATTGCCAGAG-AAAG
*
2692082 TTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATA
65 TTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
2692134 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGTC-TTTCCAGAGAAAG
1 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAATTGATGGATCA-TCATTGCCAGAGAAAG
2692198 TTCATAATGAGAAGAA--CTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
65 TTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
2692247 AGAAGAGCTTGTTCAACCTTT
1 AGAAGAACTTGTTCAACCTTT
2692268 GTTTGATGTT
Statistics
Matches: 335, Mismatches: 22, Indels: 21
0.89 0.06 0.06
Matches are distributed among these distances:
113 53 0.16
114 50 0.15
115 21 0.06
116 147 0.44
117 63 0.19
118 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (115 bp):
AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAATTGATGGATCATCATTGCCAGAGAAAGT
TCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
Found at i:2692593 original size:3 final size:3
Alignment explanation
Indices: 2692585--2692685 Score: 126
Period size: 3 Copynumber: 35.7 Consensus size: 3
2692575 TTTTTATCCA
2692585 TAT TAT TAT TA- TAT TAT TA- TAT TA- TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
*
2692628 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TA- TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2692673 TA- TAT TAA TAT TA
1 TAT TAT TAT TAT TA
2692686 AATACATAAA
Statistics
Matches: 87, Mismatches: 3, Indels: 16
0.82 0.03 0.15
Matches are distributed among these distances:
2 14 0.16
3 70 0.80
4 3 0.03
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2692601 original size:8 final size:8
Alignment explanation
Indices: 2692588--2692679 Score: 120
Period size: 8 Copynumber: 11.6 Consensus size: 8
2692578 TTATCCATAT
2692588 TATTATTA
1 TATTATTA
2692596 TATTATTA
1 TATTATTA
2692604 TATTA-TA
1 TATTATTA
2692611 TTATTATTA
1 -TATTATTA
2692620 T-TTATTA
1 TATTATTA
2692627 TTATTATTA
1 -TATTATTA
2692636 TATTA-T-
1 TATTATTA
2692642 TATTATTA
1 TATTATTA
2692650 TTATTATTA
1 -TATTATTA
2692659 TATTATTA
1 TATTATTA
*
2692667 TACTATTA
1 TATTATTA
2692675 TATTA
1 TATTA
2692680 ATATTAAATA
Statistics
Matches: 75, Mismatches: 2, Indels: 14
0.82 0.02 0.15
Matches are distributed among these distances:
6 5 0.07
7 10 0.13
8 44 0.59
9 16 0.21
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTATTA
Found at i:2693221 original size:28 final size:30
Alignment explanation
Indices: 2693173--2693231 Score: 95
Period size: 28 Copynumber: 2.0 Consensus size: 30
2693163 GAGATATACA
*
2693173 ACGAGACAGAGAGACAGAAAAAAAAAAGAG
1 ACGAGACAGAGAGACAAAAAAAAAAAAGAG
2693203 ACGAGA-A-AGAGACAAAAAAAAAAAAGAG
1 ACGAGACAGAGAGACAAAAAAAAAAAAGAG
2693231 A
1 A
2693232 AATCCAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 21 0.75
29 1 0.04
30 6 0.21
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (30 bp):
ACGAGACAGAGAGACAAAAAAAAAAAAGAG
Done.