Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 39
Found at i:3877423 original size:10 final size:10
Alignment explanation
Indices: 3877394--3877445 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
3877384 TTAGGTGTTG
3877394 TATAAGCTTA
1 TATAAGCTTA
* *
3877404 AAGAAAGCTTA
1 TA-TAAGCTTA
3877415 TATAAGCTTA
1 TATAAGCTTA
* *
3877425 AAGAAAGCTTA
1 TA-TAAGCTTA
3877436 TATAAGCTTA
1 TATAAGCTTA
3877446 AAACACCAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 16 0.50
11 16 0.50
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (10 bp):
TATAAGCTTA
Found at i:3881523 original size:27 final size:28
Alignment explanation
Indices: 3881472--3881532 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
3881462 CTAATATTTT
3881472 TATATTTTATTCTATTATATATATA-TA
1 TATATTTTATTCTATTATATATATACTA
* *
3881499 TATATTTTATATC-ATTATTTTTATACGTA
1 TATATTTTAT-TCTATTATATATATAC-TA
3881528 TATAT
1 TATAT
3881533 ATACATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 20 0.69
28 2 0.07
29 7 0.24
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (28 bp):
TATATTTTATTCTATTATATATATACTA
Found at i:3881594 original size:26 final size:25
Alignment explanation
Indices: 3881538--3881599 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
3881528 TATATATACA
*
3881538 TCTATTATTTTCGTTATTTTGTATAT
1 TCTATT-TATTCGTTATTTTGTATAT
*
3881564 TCTATTTATTCGTCTATTTT-TTTAT
1 TCTATTTATTCGT-TATTTTGTATAT
3881589 TGCTATTTATT
1 T-CTATTTATT
3881600 ATGTACATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.18, C:0.10, G:0.06, T:0.66
Consensus pattern (25 bp):
TCTATTTATTCGTTATTTTGTATAT
Found at i:3881642 original size:5 final size:5
Alignment explanation
Indices: 3881632--3881834 Score: 57
Period size: 5 Copynumber: 39.6 Consensus size: 5
3881622 GATTTTCCTA
* *
3881632 TATTT TATTT TATTT T-TTCT TGTCTT TATTTT TAATTT TATTC T-TTT
1 TATTT TATTT TATTT TATT-T TAT-TT TA-TTT T-ATTT TATTT TATTT
** * ** * **
3881679 CGTTT T-GTT TATTT TATTT TGGTT TATTC TA-TT TA-TT TATTT T-CCT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
* * *
3881725 TATTT TCTTT ATTTTT TGATTT TATTT CTA-TT T-CTT TATTT TCACTTT
1 TATTT TATTT -TATTT T-ATTT TATTT -TATTT TATTT TATTT T-A-TTT
* * *
3881773 GTATTT TA-TT TACTTGT TATTAT TATTT TATTAT TATTT TTTTAT TACTC
1 -TATTT TATTT TA-TT-T TATT-T TATTT TATT-T TATTT TATT-T TATTT
3881823 T-TTT TATTT TAT
1 TATTT TATTT TAT
3881835 CTTCTTTATT
Statistics
Matches: 147, Mismatches: 28, Indels: 46
0.67 0.13 0.21
Matches are distributed among these distances:
4 26 0.18
5 70 0.48
6 40 0.27
7 10 0.07
8 1 0.01
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:3881692 original size:23 final size:23
Alignment explanation
Indices: 3881635--3881696 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
3881625 TTTCCTATAT
3881635 TTTAT-TTTATTTT-TTCTTGTC
1 TTTATGTTTATTTTATTCTTGTC
* *
3881656 TTTATTTTTAATTTTATTCTTTTC
1 TTTATGTTT-ATTTTATTCTTGTC
3881680 GTTT-TGTTTATTTTATT
1 -TTTATGTTTATTTTATT
3881697 TTGGTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 5 0.14
22 3 0.09
23 13 0.37
24 11 0.31
25 3 0.09
ACGTcount: A:0.13, C:0.06, G:0.05, T:0.76
Consensus pattern (23 bp):
TTTATGTTTATTTTATTCTTGTC
Found at i:3881803 original size:11 final size:11
Alignment explanation
Indices: 3881789--3881819 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3881779 TATTTACTTG
3881789 TTATTATTATT
1 TTATTATTATT
3881800 TTATTATTATT
1 TTATTATTATT
*
3881811 TTTTTATTA
1 TTATTATTA
3881820 CTCTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTATTATT
Found at i:3881806 original size:14 final size:14
Alignment explanation
Indices: 3881789--3881819 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3881779 TATTTACTTG
3881789 TTATTATTATTTTA
1 TTATTATTATTTTA
*
3881803 TTATTATTTTTTTA
1 TTATTATTATTTTA
3881817 TTA
1 TTA
3881820 CTCTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTATTTTA
Found at i:3887032 original size:20 final size:19
Alignment explanation
Indices: 3886995--3887055 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
3886985 GTATCGATCC
*
3886995 AAAATGAT-ATACCAGGTAA
1 AAAATGATAAAACC-GGTAA
*
3887014 AAATATGATAAAACCGGTATC
1 AAA-ATGATAAAACCGGTA-A
*
3887035 AAAATGATAAAATCGGTAA
1 AAAATGATAAAACCGGTAA
3887054 AA
1 AA
3887056 CATTACCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 5 0.14
20 23 0.66
21 7 0.20
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (19 bp):
AAAATGATAAAACCGGTAA
Found at i:3887133 original size:181 final size:180
Alignment explanation
Indices: 3886797--3887268 Score: 676
Period size: 180 Copynumber: 2.6 Consensus size: 180
3886787 GATCCAAATT
* * * * *
3886797 AAAAATGTGTCTATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
3886862 AAATCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAATCGGTAAAAC-ATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
3886927 ATGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGCTACTTTTA
130 ATGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATAC-TTTA
* *
3886979 AAAAATGTATCGATCCAAAATGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
3887044 AAATCGGTAAAACATTACCAGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAATCGGTAAAACA-TACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* ** *
3887108 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTA
130 ATGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
* * *
3887159 AAAAATATATCGATCCACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
3887224 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAATCGGTAAAA-CATACCGGATATATTGAAAGTGTCGATACTTT
3887269 CGTAAGTACG
Statistics
Matches: 260, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
180 104 0.40
181 60 0.23
182 96 0.37
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (180 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAATCGGTAAAACATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCA
TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
Found at i:3887237 original size:17 final size:19
Alignment explanation
Indices: 3887198--3887240 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3887188 AAGTAAAAAT
3887198 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
3887218 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
3887235 ATGATA
1 ATGATA
3887241 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:3889376 original size:15 final size:15
Alignment explanation
Indices: 3889356--3889384 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3889346 GTTGTATTGG
3889356 GGGATGACGGTGAGT
1 GGGATGACGGTGAGT
3889371 GGGATGACGGTGAG
1 GGGATGACGGTGAG
3889385 GGAAAACATA
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:0.21, C:0.07, G:0.55, T:0.17
Consensus pattern (15 bp):
GGGATGACGGTGAGT
Found at i:3889495 original size:21 final size:21
Alignment explanation
Indices: 3889469--3889516 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
3889459 AAGACAATCA
*
3889469 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
3889490 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
3889511 AGAGTC
1 AGAGTC
3889517 CAATATACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:3889611 original size:33 final size:33
Alignment explanation
Indices: 3889569--3889632 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
3889559 ATAGATGGAC
*
3889569 TGGTGAAAGAAGTAGAGGTCTTGAGGGGTGAAG
1 TGGTGAAAGAAGTAGAGGTCTTAAGGGGTGAAG
* * *
3889602 TGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 TGGTGAAAGAAGTAGAGGTCTTAAGGGGTGA
3889633 TATTAAGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.28, C:0.02, G:0.47, T:0.23
Consensus pattern (33 bp):
TGGTGAAAGAAGTAGAGGTCTTAAGGGGTGAAG
Found at i:3891446 original size:19 final size:19
Alignment explanation
Indices: 3891422--3891470 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
3891412 AATGTAGGGT
3891422 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3891441 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
3891460 TAATTTTGTAT
1 TAATTTTGTAT
3891471 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3892047 original size:200 final size:200
Alignment explanation
Indices: 3891704--3892144 Score: 837
Period size: 200 Copynumber: 2.2 Consensus size: 200
3891694 AATTTACAAT
* *
3891704 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCATAAACAT
*
3891769 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
3891834 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
3891899 AATGA
196 AATGA
*
3891904 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTATCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCATAAACAT
*
3891969 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
3892034 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
3892099 AATGA
196 AATGA
3892104 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATAT
3892145 CCATAAGTAT
Statistics
Matches: 236, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 236 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:3892257 original size:170 final size:173
Alignment explanation
Indices: 3891972--3892416 Score: 711
Period size: 170 Copynumber: 2.6 Consensus size: 173
3891962 TAAACATCGA
3891972 AACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
1 AACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
3892037 AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
66 AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
3892102 GAATGGCAAACAGGGTGCAACAATAAAGTGTCGAT-CCAT-AT
131 GAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCCATAAT
*
3892143 -ATCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
1 AACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
*
3892207 AGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
66 AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
*
3892272 GAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCCATAAACAT
131 GAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCCAT--A-AT
* * *
3892318 CGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
1 ---AACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
3892383 ATGGGAGAATTA-GTATATAAT-ATGTATCGACACT
63 ATGAGAGAA-TAGGTCTA-AATAATGTATCGACACT
3892417 GTTTAATGTT
Statistics
Matches: 253, Mismatches: 10, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
170 161 0.64
171 4 0.02
175 2 0.01
179 81 0.32
180 5 0.02
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (173 bp):
AACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
GAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCCATAAT
Found at i:3892914 original size:12 final size:12
Alignment explanation
Indices: 3892892--3892937 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
3892882 CAAGCGGTCA
*
3892892 ATGAAGATGAAG
1 ATGACGATGAAG
*
3892904 CTGACGATGAAG
1 ATGACGATGAAG
*
3892916 ATGACGATGATG
1 ATGACGATGAAG
*
3892928 ATGATGATGA
1 ATGACGATGA
3892938 TCCAAACAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:3892930 original size:18 final size:18
Alignment explanation
Indices: 3892892--3892937 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3892882 CAAGCGGTCA
*
3892892 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGATGACG
* *
3892910 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
*
3892928 ATGATGATGA
1 ATGAAGATGA
3892938 TCCAAACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:3894498 original size:183 final size:183
Alignment explanation
Indices: 3894148--3894732 Score: 1037
Period size: 183 Copynumber: 3.2 Consensus size: 183
3894138 CAAATTTTTC
*
3894148 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
** * *
3894213 CAAAAAGTGTCGA-ATGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAAT
66 CAAAAAGTGTCGACAT--TTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAAT
* *
3894277 ATAATCAGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
129 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
3894332 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
3894397 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATACTTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
3894462 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
3894515 ACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAAAAATGTGTCGATAACTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
3894580 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
3894645 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
3894698 ACACTTTTTAATTTTGTGTTGGTACTTTATGTCCA
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
3894733 TAATTATAAT
Statistics
Matches: 386, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
183 307 0.80
184 77 0.20
185 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:3894827 original size:120 final size:120
Alignment explanation
Indices: 3894614--3894852 Score: 424
Period size: 120 Copynumber: 2.0 Consensus size: 120
3894604 CGGAACCCAG
3894614 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
* *
3894679 AGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTTGGTACTTTATGTCCAT
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAT
* * *
3894734 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
*
3894799 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
3894853 GAATGGAAGA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 113 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.39
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAT
Found at i:3894978 original size:303 final size:303
Alignment explanation
Indices: 3894431--3895019 Score: 1106
Period size: 303 Copynumber: 1.9 Consensus size: 303
3894421 CGGAACCCAG
*
3894431 AATTATAATGTAATAGATACTTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
3894496 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAA
3894561 AAATGTGTCGATAACTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
131 AAATGTGTCGATAACTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
3894626 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
*
3894691 TATATCGACACTTTTTAATTTTGTGTTGGTACTTTATGTCCAT
261 TATATCGACACTTTTTAATATTGTGTTGGTACTTTATGTCCAT
* * *
3894734 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
* *
3894799 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAA
*
3894864 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
131 AAATGTGTCGATAACTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
3894929 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
3894994 TATATCGACACTTTTTAATATTGTGT
261 TATATCGACACTTTTTAATATTGTGT
3895020 CGCTAATTTT
Statistics
Matches: 278, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
303 278 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (303 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAA
AAATGTGTCGATAACTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTTGGTACTTTATGTCCAT
Found at i:3896672 original size:87 final size:87
Alignment explanation
Indices: 3896568--3896730 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
3896558 AAATAGGTCA
*
3896568 ATATAAGCGCTACCTATTACATTATATAAGTGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
3896633 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
* *
3896655 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
* *
3896720 TCGGTTAAATA
66 CCCGTTAAATA
3896731 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACCTATTTTATT
Found at i:3896702 original size:23 final size:23
Alignment explanation
Indices: 3896652--3896696 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3896642 TACCTATTTT
* *
3896652 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
3896675 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
3896697 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:3897966 original size:18 final size:19
Alignment explanation
Indices: 3897925--3897968 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3897915 TTTGATTCAC
*
3897925 GGAATATAAGATTACCAGTA
1 GGAATAAAAGATTACCAG-A
*
3897945 GGAATAAAAGATTATCAG-
1 GGAATAAAAGATTACCAGA
3897963 GGAATA
1 GGAATA
3897969 TGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.48, C:0.07, G:0.23, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGA
Found at i:3904969 original size:31 final size:31
Alignment explanation
Indices: 3904927--3904986 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3904917 AACTTAAAAG
* *
3904927 AGTTTTGCAATAATGAGATTTAAATAATTTT
1 AGTTTTACAATAATGAAATTTAAATAATTTT
3904958 AGTTTTACAATAATGAAATTTAAATAATT
1 AGTTTTACAATAATGAAATTTAAATAATT
3904987 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATAATGAAATTTAAATAATTTT
Found at i:3905542 original size:14 final size:14
Alignment explanation
Indices: 3905525--3905573 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
3905515 ATCTATAATA
3905525 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
3905539 TAATATT---TAAT
1 TAATATTAAAAAAT
*
3905550 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
3905563 TAATATTAAAA
1 TAATATTAAAA
3905574 TTAAAATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 2 0.07
11 6 0.22
13 6 0.22
14 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:3905543 original size:28 final size:24
Alignment explanation
Indices: 3905505--3905569 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 24
3905495 TATTTGATAT
3905505 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATAT-T-TAAT-TAAT-TTAA
*
3905534 AAAATTAATATTTAATTTATTTAA
1 AAAATTAATATTTAATTAATTTAA
3905558 AAAATTAATATT
1 AAAATTAATATT
3905570 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 16 0.46
25 3 0.09
26 4 0.11
27 1 0.03
28 5 0.14
29 6 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTAATATTTAATTAATTTAA
Found at i:3905603 original size:12 final size:12
Alignment explanation
Indices: 3905558--3905608 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
3905548 ATTTATTTAA
3905558 AAAATT-AATATT
1 AAAATTAAATA-T
3905570 AAAATTAAA-AT
1 AAAATTAAATAT
*
3905581 CAAA-TATAATAT
1 AAAATTA-AATAT
3905593 AAAATTAAATAT
1 AAAATTAAATAT
3905605 AAAA
1 AAAA
3905609 CATCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:3905810 original size:15 final size:15
Alignment explanation
Indices: 3905792--3905821 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3905782 GGAAAAACAA
3905792 ACACCACCATAGTCT
1 ACACCACCATAGTCT
3905807 ACACCACCATAGTCT
1 ACACCACCATAGTCT
3905822 TTAGTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.07, T:0.20
Consensus pattern (15 bp):
ACACCACCATAGTCT
Found at i:3907836 original size:2 final size:2
Alignment explanation
Indices: 3907829--3907860 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3907819 AATAAAAATG
3907829 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
3907861 GTAGGAGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3908939 original size:20 final size:20
Alignment explanation
Indices: 3908916--3908958 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3908906 TAAAACAAAT
*
3908916 AAAGGGGAG-ATAAAAAGATA
1 AAAGGAGAGAATAAAAAGA-A
*
3908936 AAAGTAGAGAATAAAAAGAA
1 AAAGGAGAGAATAAAAAGAA
3908956 AAA
1 AAA
3908959 TAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.09
Consensus pattern (20 bp):
AAAGGAGAGAATAAAAAGAA
Found at i:3908949 original size:21 final size:21
Alignment explanation
Indices: 3908925--3908988 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
3908915 TAAAGGGGAG
* *
3908925 ATAAAAAGATAAAAGTAGA-GA
1 ATAAAAAGATAAAA-TAAATAA
3908946 ATAAAAAGA-AAAATAAATAA
1 ATAAAAAGATAAAATAAATAA
3908966 ATAAAATAGATAAAA-AATATAA
1 ATAAAA-AGATAAAATAA-ATAA
3908988 A
1 A
3908989 AAATATAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 3 0.08
20 11 0.30
21 14 0.38
22 9 0.24
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.17
Consensus pattern (21 bp):
ATAAAAAGATAAAATAAATAA
Found at i:3908968 original size:20 final size:20
Alignment explanation
Indices: 3908945--3908993 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3908935 AAAAGTAGAG
3908945 AATAAAA-AGAAAAATAAATA
1 AATAAAATAGAAAAA-AAATA
*
3908965 AATAAAATAGATAAAAAATA
1 AATAAAATAGAAAAAAAATA
3908985 TAA-AAAATA
1 -AATAAAATA
3908994 TAAACAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (20 bp):
AATAAAATAGAAAAAAAATA
Found at i:3908989 original size:18 final size:19
Alignment explanation
Indices: 3908966--3909029 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 19
3908956 AAATAAATAA
*
3908966 ATAAAATAGATAAA-AAAT
1 ATAAAAAAGATAAACAAAT
*
3908984 ATAAAAAATATAAACAAAT
1 ATAAAAAAGATAAACAAAT
* *
3909003 AGTAATATAATATAAACAAAT
1 A-TAA-AAAAGATAAACAAAT
*
3909024 AGAAAA
1 ATAAAA
3909030 CCAAAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
18 12 0.32
19 6 0.16
20 5 0.13
21 15 0.39
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (19 bp):
ATAAAAAAGATAAACAAAT
Found at i:3908990 original size:9 final size:9
Alignment explanation
Indices: 3908954--3909029 Score: 57
Period size: 9 Copynumber: 8.2 Consensus size: 9
3908944 GAATAAAAAG
3908954 AAAA-ATAA
1 AAAATATAA
*
3908962 ATAA-ATAA
1 AAAATATAA
* *
3908970 AATAGATAA
1 AAAATATAA
3908979 AAAATATAA
1 AAAATATAA
3908988 AAAATATAA
1 AAAATATAA
3908997 ACAAATAGTAA
1 A-AAATA-TAA
*
3909008 TATAATATAA
1 -AAAATATAA
*
3909018 ACAAATAGAA
1 A-AAATATAA
3909028 AA
1 AA
3909030 CCAAAAAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
8 9 0.16
9 23 0.42
10 15 0.27
11 7 0.13
12 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (9 bp):
AAAATATAA
Found at i:3909015 original size:21 final size:20
Alignment explanation
Indices: 3908975--3909029 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
3908965 AATAAAATAG
3908975 ATAAA-AAATA-TAAAAAAT
1 ATAAACAAATAGTAAAAAAT
*
3908993 ATAAACAAATAGTAATATAAT
1 ATAAACAAATAGTAA-AAAAT
3909014 ATAAACAAATAG-AAAA
1 ATAAACAAATAGTAAAA
3909030 CCAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 5 0.16
19 6 0.19
20 5 0.16
21 16 0.50
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (20 bp):
ATAAACAAATAGTAAAAAAT
Found at i:3909090 original size:3 final size:3
Alignment explanation
Indices: 3909082--3909140 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
3909072 TTAAATATAT
* * * *
3909082 ATA ATA ATA ATA ATA ATA ATA GTT ATA ATA A-A A-A AGAA ATA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
3909126 ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA A
3909141 AACATCACAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 6 0.13
3 38 0.83
4 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:3909552 original size:34 final size:34
Alignment explanation
Indices: 3909512--3909583 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
3909502 ACCACCTAGC
*
3909512 CGGTCGCCGTTGACCGGTGCCGGCCACCGCTCAT
1 CGGTCGCCGTTGACCGGCGCCGGCCACCGCTCAT
3909546 CGGTCGCCGTTGACCGGCGCCGGCCACCGCTCAT
1 CGGTCGCCGTTGACCGGCGCCGGCCACCGCTCAT
3909580 CGGT
1 CGGT
3909584 AGTGGCTCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.08, C:0.42, G:0.33, T:0.17
Consensus pattern (34 bp):
CGGTCGCCGTTGACCGGCGCCGGCCACCGCTCAT
Found at i:3910340 original size:2 final size:2
Alignment explanation
Indices: 3910333--3910385 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
3910323 TAATAATACT
*
3910333 TA TA TA TA TA TA TA TG TA -A TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3910373 TA TA AA TA TA TA T
1 TA TA TA TA TA TA T
3910386 GTTTATTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3910357 original size:19 final size:19
Alignment explanation
Indices: 3910333--3910387 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
3910323 TAATAATACT
3910333 TATATATATATATATGTAA
1 TATATATATATATATGTAA
*
3910352 TATATATATATATATATAA
1 TATATATATATATATGTAA
*
3910371 TATATAAATATATATGT
1 TATATATATATATATGT
3910388 TTATTATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TATATATATATATATGTAA
Found at i:3910980 original size:37 final size:36
Alignment explanation
Indices: 3910915--3911190 Score: 111
Period size: 36 Copynumber: 8.0 Consensus size: 36
3910905 CAAAGTTTAT
* *
3910915 GTTTCAAGAGGAACTGTCTCAAGGGAGACAAAATTC
1 GTTTCAAGAGGAACTATCTCAAGAGAGACAAAATTC
* *
3910951 GTTTCAAGGGGAAACTATCTCAATAGAGACAAAATTC
1 GTTTCAAGAGG-AACTATCTCAAGAGAGACAAAATTC
* * * * * ** ***
3910988 ATTTCAAG-TGAAATGTTTTC---ACTG--TTTA-T-
1 GTTTCAAGAGGAACT-ATCTCAAGAGAGACAAAATTC
* * * *
3911017 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 GTTTCAAGAGGAACTATCTCAAGAGAGACAAAA-TTC
*
3911054 TTTTCAAG-GGAAACTATCTCAAGAGAGACAAAATTC
1 GTTTCAAGAGG-AACTATCTCAAGAGAGACAAAATTC
* * * * * *
3911090 ATTTCAAG-GGAAATGTTCTC-A-A-TGTC--TA-TC
1 GTTTCAAGAGGAACT-ATCTCAAGAGAGACAAAATTC
** * *
3911120 -TTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTC
1 GTTTCAAGAGGAACTATCTCAAGAGAGACAAAATTC
3911155 GTTTCAAG-GGAAACTATCTCAAGAGAGACAAAATTC
1 GTTTCAAGAGG-AACTATCTCAAGAGAGACAAAATTC
3911191 AATTCAAAGG
Statistics
Matches: 169, Mismatches: 49, Indels: 44
0.65 0.19 0.17
Matches are distributed among these distances:
29 21 0.12
30 10 0.06
31 2 0.01
32 3 0.02
33 4 0.02
34 3 0.02
35 9 0.05
36 61 0.36
37 56 0.33
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (36 bp):
GTTTCAAGAGGAACTATCTCAAGAGAGACAAAATTC
Found at i:3911021 original size:102 final size:101
Alignment explanation
Indices: 3910887--3911473 Score: 854
Period size: 102 Copynumber: 5.8 Consensus size: 101
3910877 ACATTTTGTG
* * * *
3910887 TTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGGAACTGTCTCAAGGGAGACAAAA-TTC
1 TTTCAAGGGAAATGTTTTC-ATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
3910951 GTTTCAAGGGGAAACTATCTCAATAGAGACAAAATTCA
65 GTTTCAA-GGGAAACTATCTCAAGAGAGACAAAATTCA
*
3910989 TTTCAAGTGAAATGTTTTCACTGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCA-TGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
3911054 TTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * * * *
3911091 TTTCAAGGGAAATGTTCTCAATGTCTATCTTTCAAGAAAAACTGTCTCAAGGGAGACAAAA-TTC
1 TTTCAAGGGAAATGTTTTC-ATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
3911155 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * * * * * *
3911192 ATTCAAAGGAAATGTTTTTGATGTTTACGTTCCAAGGGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATG-TTTTCATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
3911257 GTTTCAAGGGAAACTATCTTAAGAGAGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
3911294 TTTCAAGGGAAATGTTTTCGATGTTTATGTTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTC-ATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
* * *
3911359 GTTTTAAGAGAAATTATCTCAAGAGAGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
3911396 TTTCAATGGAAATGTTTTCGATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTC-ATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
* *
3911461 GTTTTAAGAGAAA
65 GTTTCAAGGGAAA
3911474 AAATCTTGAG
Statistics
Matches: 438, Mismatches: 41, Indels: 12
0.89 0.08 0.02
Matches are distributed among these distances:
101 89 0.20
102 340 0.78
103 9 0.02
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:3911175 original size:65 final size:65
Alignment explanation
Indices: 3911055--3911176 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 65
3911045 CAAAATTTTT
** *
3911055 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTCTCAATGTCTATC
1 TTTCAAGAAAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGATCTCAATGTCTATC
* * *
3911120 TTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACT-ATCTCAA
1 TTTCAAGAAAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-TGATCTCAA
3911177 GAGAGACAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
65 49 0.98
66 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (65 bp):
TTTCAAGAAAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGATCTCAATGTCTATC
Found at i:3911274 original size:37 final size:36
Alignment explanation
Indices: 3911224--3911305 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 36
3911214 GTTTACGTTC
* **
3911224 CAAGGGAAACTATCTCAAGGGAGACAAAATTTTGTTT
1 CAAGGGAAACTATCTCAAGAGAGACAAAA-TTCATTT
*
3911261 CAAGGGAAACTATCTTAAGAGAGACAAAATTCATTT
1 CAAGGGAAACTATCTCAAGAGAGACAAAATTCATTT
3911297 CAAGGGAAA
1 CAAGGGAAA
3911306 TGTTTTCGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 14 0.34
37 27 0.66
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (36 bp):
CAAGGGAAACTATCTCAAGAGAGACAAAATTCATTT
Found at i:3912740 original size:83 final size:88
Alignment explanation
Indices: 3912635--3912860 Score: 252
Period size: 95 Copynumber: 2.6 Consensus size: 88
3912625 TGCTAGCTAG
* *
3912635 ATCCATAAAGCTGGGACT-TTTAACCAATTGCTCTAGAGGGACAACTCAA-T-AT-GTA-AAT-A
1 ATCCATAAAGCCGGG-GTGTTTAACCAATTGCTCTAGAGGGACAACTCAATTAATAGTATAATAA
* *
3912694 CCTTTATCAGGTTAGCTGAATCTT
65 CCTTTATCAGGCTAGCTGAATATT
*
3912718 ATCCATAAAGCCGGGGTGTTTAACCAATTTC-CTTAGAGGGACAACTCAAGCTTTATTACATAGT
1 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-----ATTA-ATAGT
3912782 ATAATAACCTTTATCAGGCTAGCTGAATATT
58 ATAATAACCTTTATCAGGCTAGCTGAATATT
* *
3912813 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGA-GGATAACTCAA
1 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAA
3912861 GCTTTATTTG
Statistics
Matches: 120, Mismatches: 8, Indels: 25
0.78 0.05 0.16
Matches are distributed among these distances:
82 2 0.02
83 40 0.33
84 1 0.01
88 1 0.01
89 1 0.01
90 1 0.01
92 2 0.02
93 4 0.03
94 11 0.09
95 56 0.47
96 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (88 bp):
ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAATTAATAGTATAATAAC
CTTTATCAGGCTAGCTGAATATT
Found at i:3912882 original size:95 final size:95
Alignment explanation
Indices: 3912693--3912868 Score: 284
Period size: 95 Copynumber: 1.9 Consensus size: 95
3912683 ATATGTAAAT
* * * *
3912693 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGTGTTTAACCAATTTCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
3912758 ACAACTCAAGCTTTATTACATAGTATAATA
66 ACAACTCAAGCTTTATTACATAGTATAATA
3912788 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG-CTCTAGA-G
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGAGG
*
3912851 GATAACTCAAGCTTTATT
65 GACAACTCAAGCTTTATT
3912869 TGATATATCT
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
94 20 0.27
95 55 0.73
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTACATAGTATAATA
Found at i:3916993 original size:34 final size:32
Alignment explanation
Indices: 3916953--3917023 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 32
3916943 GGAAAATGAT
3916953 AAAAAATAAATAAAGA-AAATCGAAATAAAGTAAA
1 AAAAAATAAAT-AAGATAAAT-GAAATAAA-TAAA
* * *
3916987 AAAAAATGAATAAGATAGATGAAATGAATAAA
1 AAAAAATAAATAAGATAAATGAAATAAATAAA
3917019 AAAAA
1 AAAAA
3917024 TAATAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.27
33 11 0.33
34 13 0.39
ACGTcount: A:0.72, C:0.01, G:0.11, T:0.15
Consensus pattern (32 bp):
AAAAAATAAATAAGATAAATGAAATAAATAAA
Found at i:3917143 original size:22 final size:20
Alignment explanation
Indices: 3917095--3917168 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
3917085 TGAATAAATA
3917095 AATAAAACAAATAAAAGAGAG
1 AATAAAA-AAATAAAAGAGAG
*
3917116 -ATAAAAAGATAAAAGTAGAG
1 AATAAAAAAATAAAAG-AGAG
* *
3917136 AATAAAAATA-AAAAGA-AA
1 AATAAAAAAATAAAAGAGAG
*
3917154 AATAAATAAATAAAA
1 AATAAAAAAATAAAA
3917169 TAGAAAAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
18 9 0.20
19 13 0.29
20 15 0.33
21 8 0.18
ACGTcount: A:0.74, C:0.01, G:0.11, T:0.14
Consensus pattern (20 bp):
AATAAAAAAATAAAAGAGAG
Found at i:3917146 original size:19 final size:18
Alignment explanation
Indices: 3917103--3917168 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
3917093 TAAATAAAAC
3917103 AAATAAAAGAGAGATAAA
1 AAATAAAAGAGAGATAAA
3917121 AAGATAAAAGTAGAGA-ATAA
1 AA-ATAAAAG-AGAGATA-AA
* *
3917141 AAATAAAAAGAAAAATAAA
1 AAAT-AAAAGAGAGATAAA
3917160 TAAATAAAA
1 -AAATAAAA
3917169 TAGAAAAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 2 0.05
19 19 0.47
20 19 0.47
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (18 bp):
AAATAAAAGAGAGATAAA
Found at i:3917175 original size:21 final size:22
Alignment explanation
Indices: 3917136--3917227 Score: 84
Period size: 21 Copynumber: 4.3 Consensus size: 22
3917126 AAAAGTAGAG
*
3917136 AATAAAAATAAAA-AGAAAAAT
1 AATATAAATAAAATAGAAAAAT
*
3917157 AA-ATAAATAAAATAGAAAAAC
1 AATATAAATAAAATAGAAAAAT
* * *
3917178 AATATAAA-CAAATAGTAATAT
1 AATATAAATAAAATAGAAAAAT
*
3917199 AATATAAAGAAATATAG-AAAAT
1 AATATAAATAAA-ATAGAAAAAT
*
3917221 AAAATAA
1 AATATAA
3917228 GAAATATAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
20 9 0.16
21 28 0.48
22 17 0.29
23 4 0.07
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (22 bp):
AATATAAATAAAATAGAAAAAT
Found at i:3917247 original size:35 final size:36
Alignment explanation
Indices: 3917194--3917262 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
3917184 AACAAATAGT
3917194 AATATAATATAAAGAAATATAGAAAATAAAATAAGA
1 AATATAATATAAAGAAATATAGAAAATAAAATAAGA
** * *
3917230 AATATAAT-TAATTAAATATATATAATAAAATAA
1 AATATAATATAAAGAAATATAGAAAATAAAATAA
3917263 TAATAATAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 21 0.72
36 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (36 bp):
AATATAATATAAAGAAATATAGAAAATAAAATAAGA
Found at i:3917490 original size:21 final size:21
Alignment explanation
Indices: 3917375--3917490 Score: 51
Period size: 21 Copynumber: 5.6 Consensus size: 21
3917365 GCGAAATAAA
**
3917375 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
3917395 AATCGCAAATC-AGTTTCCAT
1 AATCGCAACGCGATTTTCCAG
* * *
3917415 AACCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
3917436 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
3917456 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
3917478 AATCGCAACGCGA
1 AATCGCAACGCGA
3917491 ATATGAAAAT
Statistics
Matches: 68, Mismatches: 22, Indels: 11
0.67 0.22 0.11
Matches are distributed among these distances:
19 1 0.01
20 24 0.35
21 39 0.57
22 4 0.06
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:3917539 original size:20 final size:20
Alignment explanation
Indices: 3917478--3917670 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
3917468 GATTTTCCAG
* ** *
3917478 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3917498 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3917518 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* **
3917538 AATCGTAACATGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3917558 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3917578 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3917598 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
3917618 AATCACAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
3917639 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3917659 AATCGCAACGCG
1 AATCGCAACGCG
3917671 ATTTTTAAAG
Statistics
Matches: 145, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.01
20 126 0.87
21 18 0.12
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3918089 original size:33 final size:33
Alignment explanation
Indices: 3918050--3918120 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3918040 TTCACTTAGA
3918050 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3918083 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3918116 TTTCA
1 TTTCA
3918121 AGTTAGTATT
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:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3918259 original size:14 final size:14
Alignment explanation
Indices: 3918240--3918296 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3918230 GAAAAATGAA
3918240 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3918254 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3918273 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3918287 AATCGCAACG
1 AATCGCAACG
3918297 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3918271 original size:33 final size:33
Alignment explanation
Indices: 3918233--3918312 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
3918223 GCAACGAGAA
3918233 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
3918266 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
3918299 AAACCAAAATCGCA
1 AAATGAAAATCGCA
3918313 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:3918349 original size:14 final size:14
Alignment explanation
Indices: 3918330--3918385 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
3918320 TTTCATTTCA
3918330 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3918344 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
3918362 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3918376 CGTTGCGATT
1 CGTTGCGATT
3918386 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 20 0.56
15 3 0.08
17 3 0.08
18 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3918360 original size:32 final size:33
Alignment explanation
Indices: 3918313--3918435 Score: 149
Period size: 32 Copynumber: 3.5 Consensus size: 33
3918303 CAAAATCGCA
3918313 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
3918346 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
3918378 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCACGTT--G-C-G--ATTCTCTCG
3918419 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
3918436 ACCAAAAGAC
Statistics
Matches: 78, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
32 31 0.40
33 11 0.14
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.27
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
Found at i:3918396 original size:21 final size:21
Alignment explanation
Indices: 3918370--3918434 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3918360 CGCGTTGCGA
3918370 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3918391 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3918411 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
3918432 TTC
1 TTC
3918435 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3918431 original size:20 final size:20
Alignment explanation
Indices: 3918369--3918432 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
3918359 TCGCGTTGCG
3918369 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
3918389 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
3918410 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
3918430 ATT
1 ATT
3918433 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3920257 original size:93 final size:93
Alignment explanation
Indices: 3920098--3920413 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
3920088 TAGATTGCTT
*
3920098 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3920163 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3920191 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3920256 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3920284 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3920349 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3920377 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
3920414 AATACCCTGA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3920567 original size:19 final size:19
Alignment explanation
Indices: 3920543--3920601 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
3920533 GCAACGAGAG
3920543 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
3920562 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
3920576 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
3920595 AATCGCA
1 AATCGCA
3920602 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.51
ACGTcount: A:0.47, C:0.31, G:0.15, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:3920569 original size:33 final size:33
Alignment explanation
Indices: 3920511--3920601 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 33
3920501 TAGTTTACTT
* * * *
3920511 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAAAA
3920545 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
3920578 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
3920602 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 40 0.75
34 13 0.25
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAAAA
Found at i:3920578 original size:14 final size:14
Alignment explanation
Indices: 3920527--3920585 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
3920517 CACGAAACTT
*
3920527 AAAATCGCAACGAG
1 AAAATCGCAACGAC
*
3920541 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
3920560 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3920574 AAAATCGCAACG
1 AAAATCGCAACG
3920586 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 9 0.24
ACGTcount: A:0.47, C:0.27, G:0.19, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3920619 original size:19 final size:19
Alignment explanation
Indices: 3920597--3920769 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
3920587 GAAACCAAAA
*
3920597 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3920616 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3920630 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3920649 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
3920665 T--CGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3920682 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
3920701 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
3920720 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
3920739 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3920759 TCGTGTTGCGA
1 TCGCGTTGCGA
3920770 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 16 0.13
16 8 0.06
17 8 0.06
19 80 0.65
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3920727 original size:38 final size:38
Alignment explanation
Indices: 3920597--3920769 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
3920587 GAAACCAAAA
*
3920597 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
3920632 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* * **
3920665 T--CGTTGTGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
3920701 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
3920739 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
3920770 AAGTAAACTA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 51 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 43 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:3922224 original size:14 final size:14
Alignment explanation
Indices: 3922205--3922240 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3922195 ATTTTTTAAT
3922205 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3922219 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3922233 TGATTTGT
1 TGATTTGT
3922241 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:3922363 original size:19 final size:19
Alignment explanation
Indices: 3922347--3922444 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
3922337 AAAAATGACT
*
3922347 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3922366 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3922385 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3922399 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3922418 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3922438 ATCGCAA
1 ATCGCAA
3922445 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.54
20 16 0.23
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3922476 original size:53 final size:53
Alignment explanation
Indices: 3922347--3922463 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
3922337 AAAAATGACT
*
3922347 ATCGCAATGTGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
3922399 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
3922452 ATCGCAATGCGA
1 ATCGCAATGCGA
3922464 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 28 0.44
53 35 0.56
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:3922516 original size:14 final size:14
Alignment explanation
Indices: 3922497--3922551 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3922487 CATTTCCGCA
3922497 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
3922511 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
3922528 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
3922544 TTGCGATT
1 TTGCGATT
3922552 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:3922529 original size:86 final size:86
Alignment explanation
Indices: 3922439--3922615 Score: 273
Period size: 86 Copynumber: 2.1 Consensus size: 86
3922429 GAAATGAAAA
3922439 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
3922504 TCTCTCGTTGCGATTTTCATT
66 TCTCTCGTTGCGATTTTCATT
** * *** * **
3922525 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
3922590 TCTCTCGTTGCGATTTTCATT
66 TCTCTCGTTGCGATTTTCATT
3922611 TCGCA
1 TCGCA
3922616 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.41
Consensus pattern (86 bp):
TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
TCTCTCGTTGCGATTTTCATT
Found at i:3922535 original size:33 final size:33
Alignment explanation
Indices: 3922477--3922570 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
3922467 TCATTTCGCA
3922477 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
3922511 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
3922544 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
3922571 TTCATTTCCG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 45 0.75
34 15 0.25
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:3922616 original size:86 final size:89
Alignment explanation
Indices: 3922459--3922667 Score: 361
Period size: 86 Copynumber: 2.3 Consensus size: 89
3922449 AGAATCGCAA
3922459 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
3922524 TTCGCATTGCGA-TTC-TCTCG-T
66 TTCGCATTGCGATTTCATCTCGAT
3922545 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
3922610 TTCGCATTGCGATTTTCATTTCGCAT
66 TTCGCATTGCGA-TTTCATCTCG-AT
3922636 TGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCAT
3922668 GTTGGGATTT
Statistics
Matches: 116, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
86 77 0.66
88 3 0.03
89 4 0.03
91 15 0.13
92 17 0.15
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (89 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTCATCTCGAT
Found at i:3922677 original size:72 final size:72
Alignment explanation
Indices: 3922462--3922695 Score: 297
Period size: 72 Copynumber: 3.3 Consensus size: 72
3922452 ATCGCAATGC
*
3922462 GATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TCT-CG--TTGCGATTTT
1 GATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCATTGCGATTTT
*
3922521 CAT-TTCG
65 CATGTTGG
* * * * *
3922528 CA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTC
1 GATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT
*
3922592 TC-TCGTTGC
64 TCAT-GTTGG
3922601 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
3922666 ATGTTGG
66 ATGTTGG
3922673 GATTTTCATTTCGCATTGCGATT
1 GATTTTCATTTCGCATTGCGATT
3922696 CTCTCGTTGC
Statistics
Matches: 142, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
65 3 0.02
66 14 0.10
67 18 0.13
68 3 0.02
69 2 0.01
70 2 0.01
71 1 0.01
72 89 0.63
73 7 0.05
74 3 0.02
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (72 bp):
GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
ATGTTGG
Found at i:3922717 original size:33 final size:33
Alignment explanation
Indices: 3922563--3922709 Score: 188
Period size: 33 Copynumber: 4.2 Consensus size: 33
3922553 TCATTTCGCA
3922563 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
3922597 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
3922633 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
3922669 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
3922702 TTGCGATT
1 TTGCGATT
3922710 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 32 0.32
34 29 0.29
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:3922724 original size:53 final size:52
Alignment explanation
Indices: 3922459--3922728 Score: 282
Period size: 53 Copynumber: 5.1 Consensus size: 52
3922449 AGAATCGCAA
* * *
3922459 TGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCCGCATTG-CGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTGTC-ATT-TCGCGT
* *
3922512 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTCATTTCGCGT
* *
3922564 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTGTCATTTCGCGT
* * **
3922617 TGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCCGCATTG-CGATTTTCATGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTGTC-A-TTTCGCGT
* * *
3922670 TGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGTGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTCATTT-CGCGT
3922723 TGCGAT
1 TGCGAT
3922729 AGTCAAATGC
Statistics
Matches: 188, Mismatches: 17, Indels: 24
0.82 0.07 0.10
Matches are distributed among these distances:
50 2 0.01
51 6 0.03
52 37 0.20
53 128 0.68
54 11 0.06
55 4 0.02
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTCATTTCGCGT
Found at i:3925011 original size:12 final size:12
Alignment explanation
Indices: 3924994--3925018 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3924984 TCTTCGGGGA
3924994 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3925006 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3925018 C
1 C
3925019 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3925227 original size:24 final size:24
Alignment explanation
Indices: 3925193--3925239 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3925183 CTGAAACATC
3925193 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3925217 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3925240 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:3925960 original size:20 final size:20
Alignment explanation
Indices: 3925932--3926161 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
3925922 AAATTTCAGT
* * *
3925932 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3925952 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
3925972 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3925992 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
3926012 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3926032 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3926052 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
3926072 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
3926092 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3926112 GTTGTGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
3926132 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
3926152 GTTGCGATTT
1 GTTGCGATTT
3926162 TGGAAACTGA
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:3930820 original size:20 final size:19
Alignment explanation
Indices: 3930791--3930844 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
3930781 AAACGAACAG
*
3930791 AATAAGGAAAATGATAAAAA
1 AATAAAGAAAATGA-AAAAA
*
3930811 AATAAAGAAAATCGAAATAA
1 AATAAAGAAAAT-GAAAAAA
*
3930831 AGTAAA-AAAATGAA
1 AATAAAGAAAATGAA
3930845 TAAGATAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 20 0.67
21 2 0.07
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (19 bp):
AATAAAGAAAATGAAAAAA
Found at i:3930987 original size:21 final size:20
Alignment explanation
Indices: 3930942--3931015 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
3930932 TGAATAAATA
*
3930942 AATAAAACAAATAAAAGGGAG
1 AATAAAA-AAATAAAAGAGAG
*
3930963 -ATAAAAAGATAAAAGTAGAG
1 AATAAAAAAATAAAAG-AGAG
* *
3930983 AATAAAAATA-AAAAGA-AA
1 AATAAAAAAATAAAAGAGAG
*
3931001 AATAAATAAATAAAA
1 AATAAAAAAATAAAA
3931016 TAGAAAAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.20
19 13 0.30
20 14 0.32
21 8 0.18
ACGTcount: A:0.73, C:0.01, G:0.12, T:0.14
Consensus pattern (20 bp):
AATAAAAAAATAAAAGAGAG
Found at i:3931022 original size:21 final size:21
Alignment explanation
Indices: 3930983--3931032 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3930973 AAAAGTAGAG
* *
3930983 AATAAAAATAAAAAGAAAAAT
1 AATATAAATAAAAAGAAAAAC
3931004 AA-ATAAATAAAATAGAAAAAC
1 AATATAAATAAAA-AGAAAAAC
3931025 AATATAAA
1 AATATAAA
3931033 CAAATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 11 0.44
22 5 0.20
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (21 bp):
AATATAAATAAAAAGAAAAAC
Found at i:3931040 original size:10 final size:10
Alignment explanation
Indices: 3931021--3931067 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
3931011 TAAAATAGAA
3931021 AAAC-AATAT
1 AAACAAATAT
3931030 AAACAAATAT
1 AAACAAATAT
3931040 AAACAAATAGT
1 AAACAAATA-T
*
3931051 AATA-TAATAT
1 AA-ACAAATAT
3931061 AAACAAA
1 AAACAAA
3931068 GAGAAAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 5 0.16
10 19 0.59
11 7 0.22
12 1 0.03
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (10 bp):
AAACAAATAT
Found at i:3931137 original size:35 final size:34
Alignment explanation
Indices: 3931088--3931195 Score: 107
Period size: 35 Copynumber: 3.1 Consensus size: 34
3931078 AAACATAAAG
* * *
3931088 AAATATAGAAAATAAAATAAGAAATATAATTAATT
1 AAATATATATAATAAAATAAGAAATATAA-TAATA
*
3931123 AAATATATATAATAAAATAA-TAATAATAATAATA
1 AAATATATATAATAAAATAAGAAAT-ATAATAATA
3931157 ATAATAGT-TATAATAAAA-AAGAAATA-AATAATA
1 A-AATA-TATATAATAAAATAAGAAATATAATAATA
3931190 ATAATA
1 A-AATA
3931196 AAACATCACA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
33 13 0.20
34 11 0.17
35 39 0.61
36 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (34 bp):
AAATATATATAATAAAATAAGAAATATAATAATA
Found at i:3931144 original size:3 final size:3
Alignment explanation
Indices: 3931131--3931196 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
3931121 TTAAATATAT
* *
3931131 ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA GTT ATA ATA A-A A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
3931176 AGAA ATAA ATA ATA ATA ATA A
1 A-TA AT-A ATA ATA ATA ATA A
3931197 AACATCACAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 6 0.11
3 43 0.80
4 5 0.09
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3932317 original size:105 final size:106
Alignment explanation
Indices: 3932103--3932325 Score: 279
Period size: 105 Copynumber: 2.1 Consensus size: 106
3932093 GATTGTCCAT
* * * *
3932103 AAGGACCACATATATAAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCA
1 AAGGACCACGTAGATAAATTCCTTAAGAACCATATACATATACCAAGGATCAAATAAGTGTCGCA
*
3932168 AAAGACCTCATACATGCTCCAAAGAATACATATACGTCCTG
66 AAAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
* * * *
3932209 AAGGACCACGTAGA-AAATTCCTTAAGAATCATATACATATGCTAAGGATCAAATACGTGTCGC-
1 AAGGACCACGTAGATAAATTCCTTAAGAACCATATACATATACCAAGGATCAAATAAGTGTCGCA
* * * * * *
3932272 AAAGAACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
66 AAAG-ACCTCATACATGCTCCAAAGAATACATATACGTCCCG
*
3932314 AAGGACCGCGTA
1 AAGGACCACGTA
3932326 AACCCTCGAC
Statistics
Matches: 100, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
104 4 0.04
105 84 0.84
106 12 0.12
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (106 bp):
AAGGACCACGTAGATAAATTCCTTAAGAACCATATACATATACCAAGGATCAAATAAGTGTCGCA
AAAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
Found at i:3937577 original size:105 final size:105
Alignment explanation
Indices: 3937373--3937597 Score: 297
Period size: 105 Copynumber: 2.1 Consensus size: 105
3937363 GATTGTCTAT
* * * *
3937373 AAGGACCACATATATAAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCA
1 AAGGACCACGTAGA-AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCA
3937438 AAAGACCTCATACATGCTCCAAAGAATACATATATGTCCCG
65 AAAGACCTCATACATGCTCCAAAGAATACATATATGTCCCG
* * * * *
3937479 AAGGTCCACGTAGAAAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATACGTGTCTCAA
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
* * * * * *
3937544 AGGACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
66 AAGACCTCATACATGCTCCAAAGAATACATATATGTCCCG
*
3937584 AAGGACCGCGTAGA
1 AAGGACCACGTAGA
3937598 CCCTCGACTC
Statistics
Matches: 102, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
105 91 0.89
106 11 0.11
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (105 bp):
AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
AAGACCTCATACATGCTCCAAAGAATACATATATGTCCCG
Found at i:3940811 original size:2 final size:2
Alignment explanation
Indices: 3940804--3940842 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3940794 TAATAATACT
3940804 TA TA TA 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 TA TA TA T
3940843 GTTTATTATG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3943634 original size:20 final size:21
Alignment explanation
Indices: 3943605--3943660 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
3943595 AAATGACCAA
3943605 CAAA-TTCGCAACGCGA-TCT
1 CAAATTTCGCAACGCGAGTCT
* *
3943624 CAAATTTCGCAACTC-AGTTT
1 CAAATTTCGCAACGCGAGTCT
*
3943644 CCAATTTCGCAACGCGA
1 CAAATTTCGCAACGCGA
3943661 ATATGTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.17
20 24 0.80
21 1 0.03
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (21 bp):
CAAATTTCGCAACGCGAGTCT
Found at i:3943700 original size:20 final size:20
Alignment explanation
Indices: 3943677--3943722 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3943667 AAATCGAAAC
3943677 GCGAAAGTCAAATTCGCAAA
1 GCGAAAGTCAAATTCGCAAA
*
3943697 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAA
3943717 GCGAAA
1 GCGAAA
3943723 CACAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAA
Found at i:3943860 original size:22 final size:22
Alignment explanation
Indices: 3943835--3943882 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
3943825 CAGCGATATT
3943835 CGTCCCCATCTCCGACGAAATC
1 CGTCCCCATCTCCGACGAAATC
* *
3943857 CGTCCCCTTCTCCGGCGAAATC
1 CGTCCCCATCTCCGACGAAATC
3943879 CGTC
1 CGTC
3943883 TATCTCCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.46, G:0.17, T:0.21
Consensus pattern (22 bp):
CGTCCCCATCTCCGACGAAATC
Found at i:3944323 original size:20 final size:20
Alignment explanation
Indices: 3944273--3944323 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3944263 TCGCAACGCG
* *
3944273 ATTTTAGTTTCGCGTTGCGC
1 ATTTAAGTTTCGCGTTGCGA
* * *
3944293 TTTTCATTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
3944313 ATTTAAGTTTC
1 ATTTAAGTTTC
3944324 AAAAACTACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.49
Consensus pattern (20 bp):
ATTTAAGTTTCGCGTTGCGA
Found at i:3946046 original size:21 final size:21
Alignment explanation
Indices: 3946022--3946067 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3946012 GTTAGGGGAG
* *
3946022 TTACGTGATGAGGTCGGTGCT
1 TTACGTCATGAGGTCGGTACT
3946043 TTACGTCATGAGGTCGGTACT
1 TTACGTCATGAGGTCGGTACT
3946064 TTAC
1 TTAC
3946068 ATTAAGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.35
Consensus pattern (21 bp):
TTACGTCATGAGGTCGGTACT
Found at i:3946526 original size:42 final size:42
Alignment explanation
Indices: 3946479--3946597 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
3946469 GATGCACCTA
* ** *
3946479 TCATCATTCAAGAGGCGCCTCCTATTGTTCAAGAGGCCTCTC
1 TCATCATTCAAGAGGCCCCTCCTACCGTTCAAGAGGCCCCTC
* *
3946521 TCATCA-TCGAAGAAGCCCCTCCTACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCCCTCCTACCGTTCAAGAGGCCCCTC
* * * *
3946563 TCATCGTTCCAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCATTCAAGAGGCCCCTCCTACCGTTCAAGAG
3946598 CCCGATTCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 60 0.94
43 2 0.03
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCTACCGTTCAAGAGGCCCCTC
Found at i:3946554 original size:21 final size:21
Alignment explanation
Indices: 3946530--3946600 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
3946520 CTCATCATCG
3946530 AAGAAGCCCCTCCTACCGTTC
1 AAGAAGCCCCTCCTACCGTTC
* * *
3946551 AAGAGGCCCCT-GTCATCGTTC
1 AAGAAGCCCCTCCT-ACCGTTC
* * * *
3946572 CAGAGGTCCCTCCCACCGTTC
1 AAGAAGCCCCTCCTACCGTTC
3946593 AAG-AGCCC
1 AAGAAGCCC
3946601 GATTCATATG
Statistics
Matches: 37, Mismatches: 11, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
20 4 0.11
21 33 0.89
ACGTcount: A:0.21, C:0.41, G:0.20, T:0.18
Consensus pattern (21 bp):
AAGAAGCCCCTCCTACCGTTC
Found at i:3947887 original size:65 final size:65
Alignment explanation
Indices: 3947784--3947927 Score: 254
Period size: 66 Copynumber: 2.2 Consensus size: 65
3947774 TTTTACATTG
3947784 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTA
* *
3947848 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
3947913 A
65 A
3947914 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
3947928 GTTTTAAATC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
64 17 0.22
65 19 0.25
66 40 0.53
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (65 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTA
Found at i:3947977 original size:19 final size:19
Alignment explanation
Indices: 3947953--3947996 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
3947943 TGCATTATGC
3947953 TGAAGGCAAAAAGACATGT
1 TGAAGGCAAAAAGACATGT
3947972 TGAAGGCAAAAAGACATGT
1 TGAAGGCAAAAAGACATGT
3947991 TGAAGG
1 TGAAGG
3947997 TACAAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.30, T:0.16
Consensus pattern (19 bp):
TGAAGGCAAAAAGACATGT
Found at i:3949323 original size:18 final size:18
Alignment explanation
Indices: 3949300--3949336 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3949290 CGAAATTTAT
3949300 ATTGAAATTCAAAATCAA
1 ATTGAAATTCAAAATCAA
* *
3949318 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAAATCAA
3949336 A
1 A
3949337 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAAATCAA
Found at i:3949750 original size:25 final size:25
Alignment explanation
Indices: 3949722--3949771 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3949712 CATTATTTTC
*
3949722 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
*
3949747 CAAATAATGTACCCACAATAATGTT
1 CAAATAATGTACCCACAACAATGTT
3949772 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:3949766 original size:14 final size:13
Alignment explanation
Indices: 3949721--3949770 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
3949711 ACATTATTTT
3949721 CCAAATAATGTAC
1 CCAAATAATGTAC
*
3949734 CCATAACAATGT--
1 CCA-AATAATGTAC
*
3949746 TCAAATAATGTAC
1 CCAAATAATGTAC
3949759 CCACAATAATGT
1 CCA-AATAATGT
3949771 TTAATTGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 7 0.24
12 2 0.07
13 5 0.17
14 15 0.52
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (13 bp):
CCAAATAATGTAC
Found at i:3950253 original size:6 final size:6
Alignment explanation
Indices: 3950244--3950278 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3950234 TTGTGATTGG
**
3950244 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
3950279 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:3950260 original size:18 final size:18
Alignment explanation
Indices: 3950237--3950277 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3950227 AAGTCGGTTG
*
3950237 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3950255 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
3950273 TGATT
1 TGATT
3950278 TCCTTTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3952604 original size:24 final size:24
Alignment explanation
Indices: 3952553--3952604 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3952543 ATCCTAGTAT
** *
3952553 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
3952577 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
3952601 TGAC
1 TGAC
3952605 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:3953368 original size:14 final size:15
Alignment explanation
Indices: 3953332--3953369 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3953322 TAAATCATTG
3953332 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
3953347 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
3953362 AAAAATTA
1 AAAAATTA
3953370 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:3953586 original size:19 final size:20
Alignment explanation
Indices: 3953526--3953716 Score: 126
Period size: 20 Copynumber: 9.6 Consensus size: 20
3953516 ACTAAAACCT
* *
3953526 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * *
3953545 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGA
3953565 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
*
3953584 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-CGA
* *
3953605 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
* *
3953625 GTTGCGAATTTG-ACTTCTGT
1 GTTGCGAATTTGAAATTC-GA
*
3953645 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGA-A-ATTCGA
* *
3953665 GTTGCGAATTTGGAAACT-GG
1 GTTGCGAATTT-GAAATTCGA
* * * *
3953685 GTTGCGAAATTGGAGTTCGC
1 GTTGCGAATTTGAAATTCGA
3953705 GTTGCGAATTTG
1 GTTGCGAATTTG
3953717 TTGGTCATTT
Statistics
Matches: 140, Mismatches: 20, Indels: 23
0.77 0.11 0.13
Matches are distributed among these distances:
19 36 0.26
20 80 0.57
21 22 0.16
22 1 0.01
23 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:3953609 original size:40 final size:40
Alignment explanation
Indices: 3953526--3953634 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 40
3953516 ACTAAAACCT
* * *
3953526 GTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCGA
* * *
3953565 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAAT-CGA
* *
3953605 GTTGCGAATTTG-ACTATCGCGTTGCGAATT
1 GTTGCGAATTTGAAAT-TCGAGTTGCGAATT
3953635 TGACTTCTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
39 27 0.47
40 21 0.36
41 10 0.17
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (40 bp):
GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCGA
Found at i:3953612 original size:60 final size:58
Alignment explanation
Indices: 3953526--3953637 Score: 143
Period size: 60 Copynumber: 1.9 Consensus size: 58
3953516 ACTAAAACCT
* *
3953526 GTTGCGAAATTAAATTCGTGTTGCGAATTCGAAAATCTAGTTGCGAATTTGAAATTCA
1 GTTGCGAAATTAAATTCGCGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCA
* * ** *
3953584 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGA
1 GTTGCGAAATT-AAATT-CGCGTTGCGAATTCGAAAATCGAGTTGCGAATTTGA
3953638 CTTCTGTGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 10 0.22
59 5 0.11
60 30 0.67
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (58 bp):
GTTGCGAAATTAAATTCGCGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCA
Found at i:3953825 original size:14 final size:14
Alignment explanation
Indices: 3953806--3953838 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3953796 CTCTTTATAA
3953806 AATTATTATAATAT
1 AATTATTATAATAT
*
3953820 AATTATTATATTAT
1 AATTATTATAATAT
3953834 -ATTAT
1 AATTAT
3953839 ATCATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTATTATAATAT
Found at i:3957894 original size:2 final size:2
Alignment explanation
Indices: 3957887--3957915 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3957877 AATTCTCCAT
3957887 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
3957916 TTTATGGTTT
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:3960633 original size:59 final size:59
Alignment explanation
Indices: 3960553--3960710 Score: 210
Period size: 59 Copynumber: 2.7 Consensus size: 59
3960543 ATTAGTTTAT
* * * **
3960553 AAAAAATTAGAGGCTCTTAATAATTAAGGTAGAAAGTGGAGACAATTTTATAAAATT-G
1 AAAAAAATAGAAGCCCTTAATAATTAAATTAGAAAGTGGAGACAATTTTATAAAATTGG
** * * *
3960611 AAAAATAATAGGCGCCCTTAATAATTAAATTAGAAAGTGGGGACTATTTTATGAAATTGG
1 AAAAA-AATAGAAGCCCTTAATAATTAAATTAGAAAGTGGAGACAATTTTATAAAATTGG
3960671 AAAAAAATAGAAGCCCTTAATAATTAAATTAGAAAGTGGA
1 AAAAAAATAGAAGCCCTTAATAATTAAATTAGAAAGTGGA
3960711 AACCCTAAGT
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
58 5 0.06
59 75 0.87
60 6 0.07
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (59 bp):
AAAAAAATAGAAGCCCTTAATAATTAAATTAGAAAGTGGAGACAATTTTATAAAATTGG
Found at i:3961451 original size:60 final size:60
Alignment explanation
Indices: 3961368--3961500 Score: 173
Period size: 60 Copynumber: 2.2 Consensus size: 60
3961358 TATATCATAT
*
3961368 ATCCCTAAACTATAACTCTCATTTTGA-ATTGGTCCTTAAACTCTTGAAT-ATT-TCAATTTC
1 ATCCCTAAACTATAACTCTCATTTT-ATATTAGTCCTTAAACTCTTG-ATCATTCT-AATTTC
* * * *
3961428 ATCCATAAATTATAACTCTCATTTTATATTAGTCCTTAAGCTTTTGATCATTCTAATTTC
1 ATCCCTAAACTATAACTCTCATTTTATATTAGTCCTTAAACTCTTGATCATTCTAATTTC
3961488 ATCCCTAAACTAT
1 ATCCCTAAACTAT
3961501 GACCCTCTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 3 0.05
60 59 0.94
61 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (60 bp):
ATCCCTAAACTATAACTCTCATTTTATATTAGTCCTTAAACTCTTGATCATTCTAATTTC
Found at i:3964946 original size:166 final size:162
Alignment explanation
Indices: 3964671--3965119 Score: 567
Period size: 166 Copynumber: 2.8 Consensus size: 162
3964661 CTCAACCGCG
* *
3964671 ACACTCTAGAAGAAGTAGAAAAACGAGCCCGTATACCTCTCCTATTTGAAGTATTCTGAGAAGTT
1 ACACTCTAG-AGAAGTAGAAAAACGAGCCCGTACACCTCTCCTATTTGAAGTATTCTGAGAAGTC
* * **
3964736 CGCAATGGGGACGGAGTGTGAGACTGCCTTGCTGAGCCTCTCTGCATAAGAAGCAAAGAATAATA
65 CGCAATGGAGACCGAGTACGAGACTGCCTTGCTGAGCCTCTCTGCATAAGAAGCAAAGAATAATA
*
3964801 TAACAGGAATAACTTGGCACAAATTCAGAAGGAAA
130 TAACAGGAATAACTT-GCACAAATTCA-AAAGAAA
*
3964836 AGCACTCTAGCAGAAGTAGAAAAACGAGCCCATACACCTCTCCTATTTGAAGTATTCTGAGAAGT
1 A-CACTCTAG-AGAAGTAGAAAAACGAGCCCGTACACCTCTCCTATTTGAAGTATTCTGAGAAGT
**
3964901 CCGCGGTGGAGACCGAGTACGAGACTGCCTTGCTGAGCCTCTCTGCATAAGAAGCAAAGAATAAT
64 CCGCAATGGAGACCGAGTACGAGACTGCCTTGCTGAGCCTCTCTGCATAAGAAGCAAAGAATAAT
*
3964966 ATAACAGGAGTAACTTGCACAAATTCAAAAGAAA
129 ATAACAGGAATAACTTGCACAAATTCAAAAGAAA
* * * * * *
3965000 A-A-TC-A-AG--G-A-AAATA-GAGCCCGTACTCCTCTCCTATTTGTAGAATTCTGAGACGTCT
1 ACACTCTAGAGAAGTAGAAAAACGAGCCCGTACACCTCTCCTATTTGAAGTATTCTGAGAAGTCC
* * * * * **
3965056 GTAATGAAGACTGAGTACGACACTGCCTTGTTGAGCCTCTCTG-ATTTGAAGCAAAGAATAATAT
66 GCAATGGAGACCGAGTACGAGACTGCCTTGCTGAGCCTCTCTGCATAAGAAGCAAAGAATAATAT
3965120 TACATGAGGA
Statistics
Matches: 255, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
152 19 0.07
153 72 0.28
154 4 0.02
155 1 0.00
156 1 0.00
158 2 0.01
160 1 0.00
161 2 0.01
162 1 0.00
164 7 0.03
165 12 0.05
166 133 0.52
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (162 bp):
ACACTCTAGAGAAGTAGAAAAACGAGCCCGTACACCTCTCCTATTTGAAGTATTCTGAGAAGTCC
GCAATGGAGACCGAGTACGAGACTGCCTTGCTGAGCCTCTCTGCATAAGAAGCAAAGAATAATAT
AACAGGAATAACTTGCACAAATTCAAAAGAAA
Found at i:3971056 original size:25 final size:25
Alignment explanation
Indices: 3971028--3971085 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
3971018 ATGAAAATTT
*
3971028 ATTTCCCCTTTGACCGAGCTATCTC
1 ATTTCCCCTTTGACCGAACTATCTC
3971053 ATTTCCCCTTTGACCGAACTATCTC
1 ATTTCCCCTTTGACCGAACTATCTC
3971078 ATTTCCCC
1 ATTTCCCC
3971086 CCAAATTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.17, C:0.38, G:0.09, T:0.36
Consensus pattern (25 bp):
ATTTCCCCTTTGACCGAACTATCTC
Found at i:3974544 original size:33 final size:32
Alignment explanation
Indices: 3974502--3974568 Score: 125
Period size: 33 Copynumber: 2.1 Consensus size: 32
3974492 TCTTTTAAAG
3974502 ATTTAAAAAGTTTATTCGATTTTTTGAAGATAT
1 ATTTAAAAAGTTTATTCGATTTTTTGAAGA-AT
3974535 ATTTAAAAAGTTTATTCGATTTTTTGAAGAAT
1 ATTTAAAAAGTTTATTCGATTTTTTGAAGAAT
3974567 AT
1 AT
3974569 CTTTTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 4 0.12
33 30 0.88
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (32 bp):
ATTTAAAAAGTTTATTCGATTTTTTGAAGAAT
Found at i:3974628 original size:3 final size:3
Alignment explanation
Indices: 3974622--3974888 Score: 244
Period size: 3 Copynumber: 90.0 Consensus size: 3
3974612 ATTATTATTA
3974622 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3974670 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
** * * * * * * ** ** * * *
3974718 TTC TTC GGAC -AC TAC CT- TTA GTC ATC ATAA TAAA TAC TT- TTT TTAA
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC -TTC T-TC TTC TTC TTC TT-C
*** ***
3974764 AGG AAA TATC TTC TTC TTC TTC TTC TTC TTC TT- TTC TT- TTC -TC
1 TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3974807 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3974854 TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3974889 GGACACTACC
Statistics
Matches: 229, Mismatches: 22, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
2 15 0.07
3 209 0.91
4 5 0.02
ACGTcount: A:0.07, C:0.30, G:0.02, T:0.61
Consensus pattern (3 bp):
TTC
Found at i:3975020 original size:3 final size:3
Alignment explanation
Indices: 3975012--3975051 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
3975002 CTACAAAAAT
*
3975012 ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3975052 GAGTAAAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3975435 original size:3 final size:3
Alignment explanation
Indices: 3975427--3975510 Score: 161
Period size: 3 Copynumber: 28.3 Consensus size: 3
3975417 TACTTTACCC
3975427 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3975474 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3975511 TAGGCTTAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.03
3 78 0.98
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3977864 original size:25 final size:25
Alignment explanation
Indices: 3977836--3977887 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3977826 CCGTCCTCGC
*
3977836 CTGTATCTCACGTTCCTTTTGTTCT
1 CTGTATCTCACGCTCCTTTTGTTCT
3977861 CTGTATCTCACGCTCCTTTTGTTCT
1 CTGTATCTCACGCTCCTTTTGTTCT
3977886 CT
1 CT
3977888 ATACAATCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.08, C:0.31, G:0.12, T:0.50
Consensus pattern (25 bp):
CTGTATCTCACGCTCCTTTTGTTCT
Found at i:3983094 original size:25 final size:25
Alignment explanation
Indices: 3983060--3983109 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3983050 GGAATGCATG
3983060 AACATTATGTATATTTAAGCTCAAT
1 AACATTATGTATATTTAAGCTCAAT
3983085 AACATTATGTATATTTAAGCTCAAT
1 AACATTATGTATATTTAAGCTCAAT
3983110 GACAAGCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (25 bp):
AACATTATGTATATTTAAGCTCAAT
Found at i:3986737 original size:171 final size:172
Alignment explanation
Indices: 3986452--3986795 Score: 681
Period size: 171 Copynumber: 2.0 Consensus size: 172
3986442 GGTATTCAAA
3986452 CAGACACAACAAACTTCGATTTAGTCCTAGAATCGACTAAACAGATGAAATGTATGATTATAGTT
1 CAGACACAACAAACTTCGATTTAGTCCTAGAATCGACTAAACAGATGAAATGTATGATTATAGTT
3986517 TAAGCTCAATGACAAACGAAAATGCTTATGGTTGCACTTAGGTTGCTTTCCCTGTGGTTCCAACA
66 TAAGCTCAATGACAAACGAAAATGCTTATGGTTGCACTTAGGTTGCTTTCCCTGTGGTTCCAACA
3986582 GTCAGAGTG-TGGTATGTTTCACCAAGTTTGAAGAATTGCAG
131 GTCAGAGTGTTGGTATGTTTCACCAAGTTTGAAGAATTGCAG
3986623 CAGACACAACAAACTTCGATTTAGTCCTAGAATCGACTAAACAGATGAAATGTATGATTATAGTT
1 CAGACACAACAAACTTCGATTTAGTCCTAGAATCGACTAAACAGATGAAATGTATGATTATAGTT
3986688 TAAGCTCAATGACAAACGAAAATGCTTATGGTTGCACTTAGGTTGCTTTCCCTGTGGTTCCAACA
66 TAAGCTCAATGACAAACGAAAATGCTTATGGTTGCACTTAGGTTGCTTTCCCTGTGGTTCCAACA
3986753 GTCAGAGTGTTGGTATGTTTCACCAAGTTTGAAGAATTGCAG
131 GTCAGAGTGTTGGTATGTTTCACCAAGTTTGAAGAATTGCAG
3986795 C
1 C
3986796 CGGTGGGCGA
Statistics
Matches: 172, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
171 139 0.81
172 33 0.19
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (172 bp):
CAGACACAACAAACTTCGATTTAGTCCTAGAATCGACTAAACAGATGAAATGTATGATTATAGTT
TAAGCTCAATGACAAACGAAAATGCTTATGGTTGCACTTAGGTTGCTTTCCCTGTGGTTCCAACA
GTCAGAGTGTTGGTATGTTTCACCAAGTTTGAAGAATTGCAG
Done.