Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 55
Found at i:1346121 original size:6 final size:6
Alignment explanation
Indices: 1346106--1346208 Score: 190
Period size: 6 Copynumber: 17.2 Consensus size: 6
1346096 AAATACGTAC
1346106 ATGC-A ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA
1 ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA
1346153 ATGCCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA
1 ATG-CAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA
1346202 ATGCAA A
1 ATGCAA A
1346209 AGGTGTTAAT
Statistics
Matches: 96, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.04
6 86 0.90
7 6 0.06
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGCAA
Found at i:1346474 original size:21 final size:21
Alignment explanation
Indices: 1346448--1346539 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
1346438 ATGCAAAATA
* *
1346448 GTCTTCAT-GTCTTTGTGCATG
1 GTCTTC-TCGTCTTTATGAATG
1346469 GTCTTCTCGTCTTTATGAATG
1 GTCTTCTCGTCTTTATGAATG
*
1346490 GTCTTCTCGTCTTTATGAATA
1 GTCTTCTCGTCTTTATGAATG
* * *
1346511 GTCTTCTCATCCTTGTGAATG
1 GTCTTCTCGTCTTTATGAATG
1346532 GTCTTCTC
1 GTCTTCTC
1346540 TTCCTTGGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
20 1 0.02
21 62 0.98
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
GTCTTCTCGTCTTTATGAATG
Found at i:1351594 original size:20 final size:20
Alignment explanation
Indices: 1351569--1351608 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1351559 TCAGCGTCCC
1351569 ATTTTCCACAAACATCTCTA
1 ATTTTCCACAAACATCTCTA
1351589 ATTTTCCACAAACATCTCTA
1 ATTTTCCACAAACATCTCTA
1351609 TCTCCTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTTTCCACAAACATCTCTA
Found at i:1359939 original size:83 final size:83
Alignment explanation
Indices: 1359720--1359984 Score: 325
Period size: 83 Copynumber: 3.2 Consensus size: 83
1359710 TTTAAAATGA
* * * **
1359720 CCCGAAGGATTTATTATTTTGCTCGAAAGACTTACAAATGACCCGAAATATTTCATCATCATGCT
1 CCCGAAGGACTTATCATATTGCTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCT
1359785 CGAAAGACTTACTGATGG
66 CGAAAGACTTACTGATGG
* * *
1359803 CCCGAAGGATTCTTAATCATAATGCTCGAAAGACTTACAAATGACCTGAAGGATTTCATCATCCT
1 CCCGAAGGA--CTT-ATCATATTGCTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCAT
* *
1359868 ACTCGAAAGATTTACTGATGG
63 GCTCGAAAGACTTACTGATGG
* * * * ** *
1359889 CCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATTG-CCCGAAGGATTGAAGCATCATGC
1 CCCGAAGGACTTATCATATTGCTCGAAAGACTTACA-AATGACCCGAAGGATTTCATCATCATGC
*
1359953 TCGAAAGACTTATTGATGG
65 TCGAAAGACTTACTGATGG
1359972 CCCGAAGGACTTA
1 CCCGAAGGACTTA
1359985 CTAAGTGTGA
Statistics
Matches: 155, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
83 76 0.49
84 6 0.04
85 2 0.01
86 71 0.46
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (83 bp):
CCCGAAGGACTTATCATATTGCTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCT
CGAAAGACTTACTGATGG
Found at i:1359975 original size:42 final size:43
Alignment explanation
Indices: 1359739--1359983 Score: 230
Period size: 42 Copynumber: 5.8 Consensus size: 43
1359729 TTTATTATTT
** * ** *
1359739 TGCTCGAAAGACTTACAAATGACCCGAAATA-TTTCATCATCA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTTAATCATCA
* *
1359781 TGCTCGAAAGACTTACTGATGGCCCGAAGGATTCTTAATCATAA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACT-TTAATCATCA
** * * * *
1359825 TGCTCGAAAGACTTACAAATGACCTGAAGGA-TTTCATCATCC
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTTAATCATCA
* * *
1359867 TACTCGAAAGATTTACTGATGGCCCGAAGGAC-TT-ATCATCT
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTTAATCATCA
* * * * * *
1359908 TGCTCTAAAGGCTTACAGATTGCCCGAAGGA-TTGAAGCATCA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTTAATCATCA
*
1359950 TGCTCGAAAGACTTATTGATGGCCCGAAGGACTT
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
1359984 ACTAAGTGTG
Statistics
Matches: 162, Mismatches: 35, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
41 32 0.20
42 91 0.56
43 4 0.02
44 35 0.22
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (43 bp):
TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTTAATCATCA
Found at i:1360187 original size:42 final size:41
Alignment explanation
Indices: 1360087--1360193 Score: 106
Period size: 42 Copynumber: 2.6 Consensus size: 41
1360077 ACCCGAAGGT
* * * * * *
1360087 CTTATGGATTGCCCGAAGGACTTATCATCTTGCTCTAAAGG
1 CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
* * * *
1360128 CTTACAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGA
*
1360170 CTTATTGATGGCCCGAAGGACTTA
1 CTTATAGATGGCCCGAAGGACTTA
1360194 TTAAGTGAAA
Statistics
Matches: 50, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
41 18 0.36
42 32 0.64
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:1360579 original size:217 final size:215
Alignment explanation
Indices: 1359884--1360783 Score: 1182
Period size: 217 Copynumber: 4.2 Consensus size: 215
1359874 AAGATTTACT
*
1359884 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATTG-CCCGAAGGATTGAAGCAT
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGA-TGACCCGAAGGATTTAAGCAT
* **
1359948 CATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTAAGTGTGAAAATTTGGAAATCAACTT
65 CAAGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTAAGTGTGAAAATTTGGAAATCGCCTT
* *
1360013 CTTAATTTTCAAAAATTTCATCTTCTTAAAACATCATTTTCTCA--TT----TTCATGTGAAAAC
130 CTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCACTTTCTCATTTTCAAATTCATGTGAAAAC
1360072 ATCCTACCCGAAGGTCTTATG
195 ATCCTACCCGAAGGTCTTATG
* *
1360093 GATTGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACTCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
* * * *
1360158 ATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTATTAA--GTGAAATTTTGAAAATCGCCTTC
66 AAGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTAAGTGTGAAAATTTGGAAATCGCCTTC
* *
1360221 TTAGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTCTCATTTTCAAATTCATTTGAAAACA
131 TTAGTTTTCAAAAATTTCATCTTCTTAAAACATCACTTTCTCATTTTCAAATTCATGTGAAAACA
* *
1360286 TCCTTCCCGAAGGTTTTATG
196 TCCTACCCGAAGGTCTTATG
* * *
1360306 GATGGCCCGAAGGACTTATTATCTTGCTCTAAAGGCTTATAGGTGACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
* *
1360371 AAGCTCGAAAGGCTTACTT-ATGGCCCGAAGGACTTACTAAGTTTGAAAATTTGGAAATCGCCTT
66 AAGCTCGAAAGACTTA-TTGATGGCCCGAAGGACTTACTAAGTGTGAAAATTTGGAAATCGCCTT
* *
1360435 CTTAGTTTTCAAAGATTTCATTTTCTTAAAACATCACTTTCTCATTTTCTCAAATTCATGTGAAA
130 CTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCACTTTCTCA-TTT-TCAAATTCATGTGAAA
* *
1360500 ACATCATACCCGAAGGTCTTATA
193 ACATCCTACCCGAAGGTCTTATG
* * * * * ** **
1360523 AATGGCCCAAATGACTTATCATCTTACTCTAAAGGTTTACAGATGACCTAAAGGATTTACTCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
* * * * *
1360588 ACA-CTCGAAAGACTTAATGATGGGCCGAAGGACTT-GTATAGCGCG-AAATATTGGAAATCGCC
66 A-AGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTA-AGTGTGAAAAT-TTGGAAATCGCC
* * * *
1360650 TTCTTACTTTT-AAAATATTTCATTTTCTTAAAATAAT-ACTTTCTCATTTTTCAATTTCATGTG
128 TTCTTAGTTTTCAAAA-ATTTCATCTTCTTAAAA-CATCACTTTCTCA-TTTTCAAATTCATGTG
*
1360713 AAAATATCCTACCCGAAGGTCTTATG
190 AAAACATCCTACCCGAAGGTCTTATG
* **
1360739 GATGGCCCGAAGGACTTATCATCTTACTCTAAAGAATTACAGATG
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATG
1360784 GATTTGCTTC
Statistics
Matches: 611, Mismatches: 62, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
207 61 0.10
208 2 0.00
209 100 0.16
213 125 0.20
214 2 0.00
215 60 0.10
216 88 0.14
217 170 0.28
218 3 0.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (215 bp):
GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
AAGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTAAGTGTGAAAATTTGGAAATCGCCTTC
TTAGTTTTCAAAAATTTCATCTTCTTAAAACATCACTTTCTCATTTTCAAATTCATGTGAAAACA
TCCTACCCGAAGGTCTTATG
Found at i:1362502 original size:12 final size:12
Alignment explanation
Indices: 1362481--1362510 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1362471 GGTGGACCAC
1362481 TATGGCACTAAG
1 TATGGCACTAAG
*
1362493 TATGGGACTAAG
1 TATGGCACTAAG
1362505 TATGGC
1 TATGGC
1362511 TCTTTCTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (12 bp):
TATGGCACTAAG
Found at i:1363812 original size:20 final size:20
Alignment explanation
Indices: 1363789--1363837 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
1363779 AGATCAATAA
1363789 AAAAAATAA-AAAAATATGTC
1 AAAAAATAAGAAAAA-ATGTC
1363809 AAAAACA-AAGAAAAAATGTC
1 AAAAA-ATAAGAAAAAATGTC
1363829 ATAAAAATA
1 A-AAAAATA
1363838 GAGTTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.16
Consensus pattern (20 bp):
AAAAAATAAGAAAAAATGTC
Found at i:1364940 original size:31 final size:31
Alignment explanation
Indices: 1364902--1365014 Score: 172
Period size: 31 Copynumber: 3.6 Consensus size: 31
1364892 AGACGTTAAG
1364902 TTGATGTTTTATTTAAAATTTAAGGGTTGAA
1 TTGATGTTTTATTTAAAATTTAAGGGTTGAA
*
1364933 TTGATGTTTTATTTAAAGTTTAAGGGTTGAA
1 TTGATGTTTTATTTAAAATTTAAGGGTTGAA
* *
1364964 TTGATGTTTTATTTAAAATTTAAAGGTTAAA
1 TTGATGTTTTATTTAAAATTTAAGGGTTGAA
* * *
1364995 TTTATATTTTATCTAAAATT
1 TTGATGTTTTATTTAAAATT
1365015 GAGTCTGATT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.50
Consensus pattern (31 bp):
TTGATGTTTTATTTAAAATTTAAGGGTTGAA
Found at i:1365192 original size:2 final size:2
Alignment explanation
Indices: 1365168--1365461 Score: 105
Period size: 2 Copynumber: 157.0 Consensus size: 2
1365158 TTTTAATACA
* *
1365168 AT AT AGT AT -T AT A- AT AT AT -T AT AT AT -T AT TT CAT AT AGC
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A-T
*
1365207 AT AT AT -T AT AT AGT AT AT AGT AT GAT AT -T AT AT AGC AT AT AT
1 AT AT AT AT AT AT A-T AT AT A-T AT -AT AT AT AT AT A-T AT AT AT
* * * *
1365249 AT -T AT A- AT AT TT AT AT AGT AT GT AGT AT -T AT GT AT -T AT GT
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT
* *
1365289 TT AT AT -T AT AT AT -T AT A- AT AT AT AT AT A- AC AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1365326 -T AT AT AGT AT AT -T AT -T AT AT AT AT -T AC A- AT AT -T AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1365363 -T AT AT AT -T AT AT ACT AT AT GT -T AT AT GT -T AT GT -T AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1365401 AT AT -T AGT AT AT AT AT -T A- AT GT -T AT AT ACT AT AT -T AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
*
1365440 AT AT TT AT AT -T AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
1365462 TATTTATTTA
Statistics
Matches: 223, Mismatches: 23, Indels: 92
0.66 0.07 0.27
Matches are distributed among these distances:
1 33 0.15
2 167 0.75
3 23 0.10
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1365193 original size:7 final size:7
Alignment explanation
Indices: 1365168--1365469 Score: 146
Period size: 7 Copynumber: 43.0 Consensus size: 7
1365158 TTTTAATACA
*
1365168 ATATAGT
1 ATATATT
*
1365175 AT-TATA
1 ATATATT
1365181 ATATATT
1 ATATATT
1365188 ATATATT
1 ATATATT
*
1365195 AT-T-TC
1 ATATATT
**
1365200 ATATAGC
1 ATATATT
1365207 ATATATT
1 ATATATT
*
1365214 ATATAGT
1 ATATATT
*
1365221 ATATAGT
1 ATATATT
1365228 ATGATATT
1 AT-ATATT
*
1365236 ATATAGCAT
1 ATATA--TT
1365245 ATATATT
1 ATATATT
1365252 ATAATATTT
1 AT-ATA-TT
*
1365261 ATATAGT
1 ATATATT
* *
1365268 ATGTAGT
1 ATATATT
1365275 AT-TATGT
1 ATATAT-T
1365282 AT-TATGT
1 ATATAT-T
*
1365289 TTATATT
1 ATATATT
1365296 ATATATT
1 ATATATT
1365303 ATAATATAT
1 AT-ATAT-T
**
1365312 ATATAAC
1 ATATATT
1365319 ATATAATT
1 ATAT-ATT
*
1365327 ATATAGT
1 ATATATT
1365334 ATATTATT
1 ATA-TATT
1365342 ATATA-T
1 ATATATT
* *
1365348 ATTACAAT
1 A-TATATT
1365356 ATTATATT
1 A-TATATT
1365364 ATATATT
1 ATATATT
*
1365371 ATATACT
1 ATATATT
*
1365378 ATATGTT
1 ATATATT
*
1365385 ATATGTT
1 ATATATT
*
1365392 ATGT-TAT
1 ATATAT-T
1365399 ATATATT
1 ATATATT
*
1365406 A-GTA-T
1 ATATATT
1365411 ATATATT
1 ATATATT
*
1365418 A-ATGTT
1 ATATATT
*
1365424 ATATACT
1 ATATATT
1365431 ATAT-TAT
1 ATATAT-T
1365438 ATATATT
1 ATATATT
1365445 -TATATT
1 ATATATT
1365451 ATA-A-T
1 ATATATT
1365456 ATATATT
1 ATATATT
*
1365463 ATTTATT
1 ATATATT
1365470 TAATCATTTC
Statistics
Matches: 232, Mismatches: 37, Indels: 52
0.72 0.12 0.16
Matches are distributed among these distances:
5 9 0.04
6 28 0.12
7 139 0.60
8 43 0.19
9 13 0.06
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (7 bp):
ATATATT
Found at i:1365469 original size:25 final size:27
Alignment explanation
Indices: 1365208--1365471 Score: 127
Period size: 27 Copynumber: 10.1 Consensus size: 27
1365198 TCATATAGCA
*
1365208 TATATTATATAGTATA-TAGTATGATA-T
1 TATATTATATACTATATTA-TAT-ATATT
*
1365235 TATA-TAGCATA-TATATTATA-ATATT
1 TATATTA-TATACTATATTATATATATT
* * *
1365260 TATATAGTATGTAGTATTATGTAT-TATGTT
1 TATAT--TATATACTA-TAT-TATATATATT
* * *
1365290 TATATTATATATTATAATATATATATAA
1 TATATTATATACTATATTATATATAT-T
* * *
1365318 CATATAAT-TA-TATAGTATAT-TA-T
1 TATATTATATACTATATTATATATATT
*
1365341 TATA-TATATTACAATATTATAT-TA--
1 TATATTATA-TACTATATTATATATATT
*
1365365 TATATTATATACTATATGT-TATAT-GT
1 TATATTATATACTATAT-TATATATATT
* *
1365391 TATGTTATATA-TATTAGTATATATATT
1 TATATTATATACTA-TATTATATATATT
* *
1365418 AATGTTATATACTATATTATATATATT
1 TATATTATATACTATATTATATATATT
1365445 TATATTATAATA-TATATTAT-T-TATT
1 TATATTAT-ATACTATATTATATATATT
1365470 TA
1 TA
1365472 ATCATTTCAT
Statistics
Matches: 187, Mismatches: 25, Indels: 52
0.71 0.09 0.20
Matches are distributed among these distances:
22 2 0.01
23 3 0.02
24 19 0.10
25 32 0.17
26 38 0.20
27 56 0.30
28 22 0.12
29 3 0.02
30 12 0.06
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (27 bp):
TATATTATATACTATATTATATATATT
Found at i:1368736 original size:21 final size:20
Alignment explanation
Indices: 1368650--1368807 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1368640 AAATGACCAA
**
1368650 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1368669 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1368689 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1368709 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1368730 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1368751 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1368771 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1368792 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1368808 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1368798 original size:20 final size:20
Alignment explanation
Indices: 1368774--1369023 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
1368764 CGATTTTCCA
** *
1368774 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
1368794 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
1368814 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1368834 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
1368854 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
1368874 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1368894 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1368914 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1368934 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1368954 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1368974 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1368994 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
1369014 AAATCACAAC
1 AAATCGCAAC
1369024 ACTGAAATTT
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:1369745 original size:24 final size:24
Alignment explanation
Indices: 1369706--1369752 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1369696 AAATTTGGTC
1369706 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1369730 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1369753 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1369944 original size:12 final size:12
Alignment explanation
Indices: 1369927--1369951 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1369917 ATATAATCCT
1369927 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1369939 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1369951 G
1 G
1369952 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1372326 original size:19 final size:19
Alignment explanation
Indices: 1372267--1372383 Score: 137
Period size: 19 Copynumber: 6.6 Consensus size: 19
1372257 GAAATGAAAA
1372267 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
1372283 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1372300 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
1372320 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1372336 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1372353 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
1372372 TCGCATTGCGAT
1 TCGCATTGCGAT
1372384 AGTCAATTTT
Statistics
Matches: 87, Mismatches: 3, Indels: 19
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.14
16 13 0.15
17 10 0.11
18 2 0.02
19 35 0.40
20 15 0.17
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1372334 original size:53 final size:52
Alignment explanation
Indices: 1372267--1372383 Score: 207
Period size: 53 Copynumber: 2.2 Consensus size: 52
1372257 GAAATGAAAA
*
1372267 TCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
*
1372320 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTTATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1372372 TCGCATTGCGAT
1 TCGCATTGCGAT
1372384 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:1372509 original size:14 final size:14
Alignment explanation
Indices: 1372490--1372526 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1372480 CATCAATTAC
1372490 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1372504 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1372518 ACAAATCAA
1 ACAAATCAA
1372527 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1374491 original size:19 final size:19
Alignment explanation
Indices: 1374451--1374566 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
1374441 TAGTTTACTT
* *
1374451 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
1374471 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1374490 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1374504 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1374523 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1374537 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1374556 TCGCAATGCGA
1 TCGCAACGCGA
1374567 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 5, Indels: 21
0.76 0.05 0.20
Matches are distributed among these distances:
14 16 0.20
16 11 0.14
17 11 0.14
19 31 0.38
20 12 0.15
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1374507 original size:14 final size:14
Alignment explanation
Indices: 1374488--1374544 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1374478 GCGAAATGAA
*
1374488 AATCGCAACGACAG
1 AATCGCAACGAAAG
1374502 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1374519 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1374535 AATCGCAACG
1 AATCGCAACG
1374545 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1374515 original size:33 final size:33
Alignment explanation
Indices: 1374469--1374561 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1374459 CGAAACTTAA
*
1374469 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1374502 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1374535 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1374562 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1374584 original size:19 final size:19
Alignment explanation
Indices: 1374562--1374690 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1374552 AAAATCGCAA
1374562 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1374581 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1374595 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1374614 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1374628 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1374647 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1374666 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1374686 TGCGA
1 TGCGA
1374691 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1374604 original size:33 final size:33
Alignment explanation
Indices: 1374562--1374653 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1374552 AAAATCGCAA
1374562 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1374595 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1374628 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1374654 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1374893 original size:93 final size:93
Alignment explanation
Indices: 1374734--1375114 Score: 708
Period size: 93 Copynumber: 4.1 Consensus size: 93
1374724 TTGAATGGAT
*
1374734 AAATTTACTCTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1374799 AGTTTAGCAGAATTGGTAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1374827 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1374892 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1374920 AAATTTACTTTCAATCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1374985 AGTTTAGCAGAATTGGCAGCAGCCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1375013 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1375078 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1375106 AAATTTACT
1 AAATTTACT
1375115 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 279 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1376838 original size:14 final size:14
Alignment explanation
Indices: 1376819--1376908 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1376809 TTGAAATGAA
1376819 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1376833 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1376850 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1376866 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1376885 AATCGCAACGAGAT
1 AATCGCAACGAGAG
1376899 AATCGCAACG
1 AATCGCAACG
1376909 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1376856 original size:33 final size:33
Alignment explanation
Indices: 1376811--1376925 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1376801 TCTTTTGGTT
1376811 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1376844 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1376877 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1376910 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1376926 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1376857 original size:19 final size:18
Alignment explanation
Indices: 1376818--1376930 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1376808 GTTGAAATGA
1376818 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1376833 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1376850 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1376866 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1376883 AAAATCGCAA--CGAGAT-
1 -AAATCGCAACGCGAGATG
*
1376899 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1376916 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1376931 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1376959 original size:19 final size:19
Alignment explanation
Indices: 1376926--1376970 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1376916 AAAATCGCAA
**
1376926 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
1376945 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
1376964 TGCGATT
1 TGCGATT
1376971 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1377025 original size:41 final size:41
Alignment explanation
Indices: 1376968--1377045 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1376958 TCGCGTTGCG
*
1376968 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
1377009 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
1377046 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:1377030 original size:20 final size:21
Alignment explanation
Indices: 1376969--1377044 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1376959 CGCGTTGCGA
1376969 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
1376990 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
1377010 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
1377031 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1377045 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:1377171 original size:33 final size:33
Alignment explanation
Indices: 1377124--1377194 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1377114 AATACTAACT
* *
1377124 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1377157 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1377190 TGAAA
1 TGAAA
1377195 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1377428 original size:22 final size:22
Alignment explanation
Indices: 1377376--1377430 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1377366 TGGTTGTGAG
**
1377376 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1377398 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1377420 GGATTTCTTCG
1 GGATTTCTTCG
1377431 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1377601 original size:20 final size:20
Alignment explanation
Indices: 1377576--1377769 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1377566 CTTTAAATAT
1377576 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1377596 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1377618 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1377637 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1377657 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1377677 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1377697 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1377717 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1377737 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1377757 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1377770 TAGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1377763 original size:60 final size:60
Alignment explanation
Indices: 1377576--1377769 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1377566 CTTTAAATAT
**
1377576 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1377637 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1377697 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1377757 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1377770 TAGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1377821 original size:21 final size:21
Alignment explanation
Indices: 1377736--1377833 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
1377726 ATTTATGTGT
* *
1377736 TCGCGTTGCGATTTTC-ATAT
1 TCGCGTTGCGATTTTCAAAAA
1377756 TCGCGTTGCGATTTT-AGAAAA
1 TCGCGTTGCGATTTTCA-AAAA
** * ** **
1377777 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTCAAAAA
* *
1377798 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAAAAA
1377819 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1377834 GGAAACTGAT
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCAAAAA
Found at i:1377829 original size:42 final size:43
Alignment explanation
Indices: 1377736--1377834 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1377726 ATTTATGTGT
*
1377736 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTAGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTAGAAAA
** *
1377777 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCA-AGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTT-AGAAAA
*
1377819 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1377835 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 8 0.17
42 35 0.74
43 4 0.09
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTAGAAAA
Found at i:1391842 original size:19 final size:19
Alignment explanation
Indices: 1391804--1391843 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1391794 ATTATTGAGC
* *
1391804 TGGTTTTTATGTTCTGTGT
1 TGGTTTTTAAGTTCTATGT
*
1391823 TGGTTTTTAAGTTTTATGT
1 TGGTTTTTAAGTTCTATGT
1391842 TG
1 TG
1391844 TAACAAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.03, G:0.25, T:0.62
Consensus pattern (19 bp):
TGGTTTTTAAGTTCTATGT
Found at i:1393639 original size:13 final size:13
Alignment explanation
Indices: 1393621--1393645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1393611 TAAACAAGTA
1393621 AAAAATAATATTT
1 AAAAATAATATTT
1393634 AAAAATAATATT
1 AAAAATAATATT
1393646 ATCGAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATAATATTT
Found at i:1394101 original size:16 final size:17
Alignment explanation
Indices: 1394080--1394117 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1394070 TTTTTAATTT
1394080 AATTACT-TAACTTTTA
1 AATTACTCTAACTTTTA
*
1394096 AATTACTCCTAATTTTTA
1 AATTACT-CTAACTTTTA
1394114 AATT
1 AATT
1394118 TATATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTACTCTAACTTTTA
Found at i:1395588 original size:2 final size:2
Alignment explanation
Indices: 1395583--1395611 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1395573 TCCATTAACT
1395583 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1395612 GGTATACAAG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1400200 original size:78 final size:78
Alignment explanation
Indices: 1400102--1400260 Score: 273
Period size: 78 Copynumber: 2.0 Consensus size: 78
1400092 CAAGCTGCGA
* ** *
1400102 GCATGGATATCTTCCATCCTCAGCTTGCCTGTTAACTTCTGAAAATACTTACCAGGTAGACTCTT
1 GCATGGATATCTTCCATCCTCAACTTGCCTGTTAACTTCTGAAAATACTTACCAAATAGACCCTT
*
1400167 GGTAAGTATGTTT
66 GGTAAGTATGTCT
1400180 GCATGGATATCTTCCATCCTCAACTTGCCTGTTAACTTCTGAAAATACTTACCAAATAGACCCTT
1 GCATGGATATCTTCCATCCTCAACTTGCCTGTTAACTTCTGAAAATACTTACCAAATAGACCCTT
1400245 GGTAAGTATGTCT
66 GGTAAGTATGTCT
1400258 GCA
1 GCA
1400261 ACTTGATCTC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (78 bp):
GCATGGATATCTTCCATCCTCAACTTGCCTGTTAACTTCTGAAAATACTTACCAAATAGACCCTT
GGTAAGTATGTCT
Found at i:1407073 original size:22 final size:22
Alignment explanation
Indices: 1407048--1407105 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
1407038 TGTACTTATG
* *
1407048 TTTATTTTATTTT-ATTTTATTT
1 TTTATTTTATTTTCACTGT-TTT
* *
1407070 TTTATGTTGTTTTCACTGTTTT
1 TTTATTTTATTTTCACTGTTTT
1407092 TTTATTGTTATTTT
1 TTTATT-TTATTTT
1407106 TTATTAAGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTATTTTATTTTCACTGTTTT
Found at i:1410091 original size:123 final size:124
Alignment explanation
Indices: 1409856--1410103 Score: 489
Period size: 123 Copynumber: 2.0 Consensus size: 124
1409846 CAAATTATCA
1409856 TATGATTGAGAGTAATTAAAACAGATACTACTTTATAATTATCTTAATTTAATAAAAAAATAATA
1 TATGATTGAGAGTAATTAAAACAGATACTACTTTATAATTATCTTAATTTAATAAAAAAATAATA
1409921 AAAACTCCTAACAATTAAATTTCATTTTTATTGTATGTTATTTTGTTTTTCCCTTTAAT
66 AAAACTCCTAACAATTAAATTTCATTTTTATTGTATGTTATTTTGTTTTTCCCTTTAAT
1409980 TATGATTGAGAGTAATTAAAACAGATACTACTTTATAATTATCTTAATTTAAT-AAAAAATAATA
1 TATGATTGAGAGTAATTAAAACAGATACTACTTTATAATTATCTTAATTTAATAAAAAAATAATA
1410044 AAAACTCCTAACAATTAAATTTCATTTTTATTGTATGTTATTTTGTTTTTCCCTTTAAT
66 AAAACTCCTAACAATTAAATTTCATTTTTATTGTATGTTATTTTGTTTTTCCCTTTAAT
1410103 T
1 T
1410104 TCCCCCTCAC
Statistics
Matches: 124, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
123 71 0.57
124 53 0.43
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (124 bp):
TATGATTGAGAGTAATTAAAACAGATACTACTTTATAATTATCTTAATTTAATAAAAAAATAATA
AAAACTCCTAACAATTAAATTTCATTTTTATTGTATGTTATTTTGTTTTTCCCTTTAAT
Found at i:1412189 original size:17 final size:18
Alignment explanation
Indices: 1412169--1412211 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1412159 AAAATAGTCC
1412169 TAAACGAAA-AAAACACT
1 TAAACGAAAGAAAACACT
**
1412186 TAAATAAAAGAAAACACT
1 TAAACGAAAGAAAACACT
*
1412204 TAATCGAA
1 TAAACGAA
1412212 CTAAAGAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.63, C:0.14, G:0.07, T:0.16
Consensus pattern (18 bp):
TAAACGAAAGAAAACACT
Found at i:1412336 original size:10 final size:10
Alignment explanation
Indices: 1412321--1412363 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
1412311 AAGGAGAGCG
1412321 AAAAAAATAA
1 AAAAAAATAA
1412331 AAAAAAATAA
1 AAAAAAATAA
* *
1412341 AATAAAAGAA
1 AAAAAAATAA
1412351 AATATAAAATAA
1 AA-A-AAAATAA
1412363 A
1 A
1412364 GAAATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 20 0.74
12 7 0.26
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:1412342 original size:15 final size:17
Alignment explanation
Indices: 1412324--1412367 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
1412314 GAGAGCGAAA
1412324 AAAATAAAA-AAAA-AT
1 AAAATAAAAGAAAATAT
1412339 AAAATAAAAGAAAATAT
1 AAAATAAAAGAAAATAT
1412356 AAAAT-AAAGAAA
1 AAAATAAAAGAAA
1412368 TAAAATAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.33
16 11 0.41
17 7 0.26
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAATAAAAGAAAATAT
Found at i:1412342 original size:17 final size:16
Alignment explanation
Indices: 1412323--1412363 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1412313 GGAGAGCGAA
1412323 AAAAATAAAAAAAAAT
1 AAAAATAAAAAAAAAT
*
1412339 -AAAATAAAAGAAAAT
1 AAAAATAAAAAAAAAT
1412354 ATAAAATAAA
1 A-AAAATAAA
1412364 GAAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 14 0.64
17 8 0.36
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (16 bp):
AAAAATAAAAAAAAAT
Found at i:1412352 original size:25 final size:25
Alignment explanation
Indices: 1412324--1412372 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1412314 GAGAGCGAAA
1412324 AAAATA-AAAAAAAATAAAATAAAAG
1 AAAATATAAAAAAAA-AAAATAAAAG
* *
1412349 AAAATATAAAATAAAGAAATAAAA
1 AAAATATAAAAAAAAAAAATAAAA
1412373 TAGAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.14
Consensus pattern (25 bp):
AAAATATAAAAAAAAAAAATAAAAG
Found at i:1412368 original size:15 final size:15
Alignment explanation
Indices: 1412324--1412369 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1412314 GAGAGCGAAA
* *
1412324 AAAATAAAAAAAAAT
1 AAAATAAAGAAATAT
1412339 AAAATAAAAGAAAATAT
1 AAAAT-AAAG-AAATAT
1412356 AAAATAAAGAAATA
1 AAAATAAAGAAATA
1412370 AAATAGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 10 0.37
16 7 0.26
17 10 0.37
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.15
Consensus pattern (15 bp):
AAAATAAAGAAATAT
Found at i:1412399 original size:3 final size:3
Alignment explanation
Indices: 1412391--1412415 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1412381 AAAGAAAGGG
1412391 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1412416 TATACACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1412475 original size:2 final size:2
Alignment explanation
Indices: 1412470--1412498 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1412460 GAAAAAATGA
1412470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1412499 AATGTTAGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1412658 original size:3 final size:3
Alignment explanation
Indices: 1412644--1412676 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1412634 ATAGTAAATA
1412644 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
1412677 GGGACATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1412735 original size:20 final size:21
Alignment explanation
Indices: 1412702--1412742 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1412692 GAATAAGGAA
1412702 GAAAAAATATAATAAA-AAAT
1 GAAAAAATATAATAAATAAAT
1412722 GAAAATAATA-AATAAATAAAT
1 GAAAA-AATATAATAAATAAAT
1412743 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (21 bp):
GAAAAAATATAATAAATAAAT
Found at i:1412752 original size:16 final size:16
Alignment explanation
Indices: 1412724--1412774 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1412714 TAAAAAATGA
*
1412724 AAATA-ATAAATAAAT
1 AAATATATATATAAAT
1412739 AAATATATATATAAAT
1 AAATATATATATAAAT
1412755 AAA-ATATATTATTAAAT
1 AAATATATA-TA-TAAAT
1412772 AAA
1 AAA
1412775 AAGAAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 10 0.31
16 14 0.44
17 8 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATATATATAAAT
Found at i:1412761 original size:17 final size:17
Alignment explanation
Indices: 1412705--1412775 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
1412695 TAAGGAAGAA
*
1412705 AAAATATA-ATAAAAAAT
1 AAAATATATAT-ATAAAT
*
1412722 GAAAATA-ATAAATAAAT
1 -AAAATATATATATAAAT
1412739 -AAATATATATATAAAT
1 AAAATATATATATAAAT
1412755 AAAATATAT-TATTAAAT
1 AAAATATATATA-TAAAT
1412772 AAAA
1 AAAA
1412776 AGAAAAAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
15 5 0.11
16 11 0.24
17 23 0.50
18 7 0.15
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (17 bp):
AAAATATATATATAAAT
Found at i:1417912 original size:21 final size:21
Alignment explanation
Indices: 1417894--1417934 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1417884 GGAACTTTTT
1417894 TAGTCTCTGGAAGAGCTTTCA
1 TAGTCTCTGGAAGAGCTTTCA
1417915 TAGTCTCTGGAAGAGCTTTC
1 TAGTCTCTGGAAGAGCTTTC
1417935 TCAGGTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (21 bp):
TAGTCTCTGGAAGAGCTTTCA
Found at i:1425766 original size:13 final size:13
Alignment explanation
Indices: 1425725--1425768 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1425715 AAAAAATGTA
1425725 AAAATAAATAAAAG
1 AAAATAAA-AAAAG
* *
1425739 AAAATAAATACAG
1 AAAATAAAAAAAG
*
1425752 AATATAAAAAAAG
1 AAAATAAAAAAAG
1425765 AAAA
1 AAAA
1425769 AAACCAAGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAATAAAAAAAG
Found at i:1425801 original size:13 final size:14
Alignment explanation
Indices: 1425783--1425811 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1425773 CAAGGAGAGG
1425783 AAAAAA-TAAATAA
1 AAAAAATTAAATAA
1425796 AAAAAATTAAATAA
1 AAAAAATTAAATAA
1425810 AA
1 AA
1425812 GGATATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAATTAAATAA
Found at i:1425936 original size:2 final size:2
Alignment explanation
Indices: 1425929--1425961 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1425919 AAAATATGAA
1425929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1425962 AATGTTAGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1426303 original size:22 final size:23
Alignment explanation
Indices: 1426278--1426327 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1426268 AGGGACTAAA
* *
1426278 TAAAAAGAAAA-GAAACTGGGGG
1 TAAAAAGAAAAGGAAAATCGGGG
* *
1426300 TAAATATAAAAGGAAAATCGGGG
1 TAAAAAGAAAAGGAAAATCGGGG
1426323 TAAAA
1 TAAAA
1426328 TTTGAATTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.56, C:0.04, G:0.26, T:0.14
Consensus pattern (23 bp):
TAAAAAGAAAAGGAAAATCGGGG
Found at i:1427087 original size:22 final size:22
Alignment explanation
Indices: 1427056--1427236 Score: 179
Period size: 22 Copynumber: 8.8 Consensus size: 22
1427046 GGACCATTAC
*
1427056 GTCCCTAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
*
1427078 GTCCCGAAGGACCAC----TAC
1 GTCCCGAAGGACCACTGGATAT
* **
1427096 GTCCCAAAAAACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* *
1427118 GTCTCGAAGGACCAC----TAC
1 GTCCCGAAGGACCACTGGATAT
*
1427136 GTCCTGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
*
1427158 GTCCCGAAGGACCAC----TAC
1 GTCCCGAAGGACCACTGGATAT
* *
1427176 GTACCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCACTGGATAT
1427198 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
1427220 GTCCCGAAGGACCACTG
1 GTCCCGAAGGACCACTG
1427237 TAACCCTCGA
Statistics
Matches: 127, Mismatches: 20, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
18 45 0.35
22 82 0.65
ACGTcount: A:0.29, C:0.30, G:0.23, T:0.18
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAT
Found at i:1427099 original size:40 final size:40
Alignment explanation
Indices: 1427044--1427213 Score: 252
Period size: 40 Copynumber: 4.2 Consensus size: 40
1427034 ATTTGGCCCA
*
1427044 AAGGACCATTACGTCCCTAAGGACCACTGGATATGTCCCG
1 AAGGACCACTACGTCCCTAAGGACCACTGGATATGTCCCG
* ** *
1427084 AAGGACCACTACGTCCCAAAAAACCACTGGATATGTCTCG
1 AAGGACCACTACGTCCCTAAGGACCACTGGATATGTCCCG
1427124 AAGGACCACTACGT-CCTGAAGGACCACTGGATATGTCCCG
1 AAGGACCACTACGTCCCT-AAGGACCACTGGATATGTCCCG
* * *
1427164 AAGGACCACTACGTACCGAAGGACCACTGTATATGTCCCG
1 AAGGACCACTACGTCCCTAAGGACCACTGGATATGTCCCG
1427204 AAGGACCACT
1 AAGGACCACT
1427214 GGATATGTCC
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 2 0.02
40 113 0.97
41 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.18
Consensus pattern (40 bp):
AAGGACCACTACGTCCCTAAGGACCACTGGATATGTCCCG
Found at i:1427146 original size:18 final size:17
Alignment explanation
Indices: 1427122--1427191 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 17
1427112 GGATATGTCT
1427122 CGAAGGACCACTACGTC
1 CGAAGGACCACTACGTC
*
1427139 CTGAAGGACCACTGGATATGTCC
1 C-GAAGGACCAC----TACGT-C
1427162 CGAAGGACCACTACGTAC
1 CGAAGGACCACTACGT-C
1427180 CGAAGGACCACT
1 CGAAGGACCACT
1427192 GTATATGTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
17 1 0.02
18 27 0.61
22 14 0.32
23 2 0.05
ACGTcount: A:0.30, C:0.31, G:0.24, T:0.14
Consensus pattern (17 bp):
CGAAGGACCACTACGTC
Found at i:1427172 original size:62 final size:61
Alignment explanation
Indices: 1427122--1427238 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 61
1427112 GGATATGTCT
*
1427122 CGAAGGACCAC-TACGTCCTGAAGGACCACTGGATATGTCCCGAAGGACCAC--TACGTAC
1 CGAAGGACCACTTACGTCCCGAAGGACCACTGGATATGTCCCGAAGGACCACTGTACGTAC
*
1427180 CGAAGGACCACTGTATATGTCCCGAAGGACCACTGGATATGTCCCGAAGGACCACTGTA
1 CGAAGGACCAC--T-TACGTCCCGAAGGACCACTGGATATGTCCCGAAGGACCACTGTA
1427239 ACCCTCGACT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
58 11 0.22
62 38 0.75
64 2 0.04
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (61 bp):
CGAAGGACCACTTACGTCCCGAAGGACCACTGGATATGTCCCGAAGGACCACTGTACGTAC
Found at i:1430631 original size:3 final size:3
Alignment explanation
Indices: 1430623--1430654 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1430613 GTAACCTGAA
1430623 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1430655 ACAATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1432452 original size:18 final size:19
Alignment explanation
Indices: 1432429--1432467 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1432419 TTTAAGTAGT
*
1432429 AATAAAAACGATTAAA-TA
1 AATAAAAACAATTAAAGTA
*
1432447 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
1432466 AA
1 AA
1432468 AAATAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:1434176 original size:21 final size:22
Alignment explanation
Indices: 1434152--1434221 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 22
1434142 TTTTCCTCTC
*
1434152 TTTTTCTTTCGAACAACCCTTT
1 TTTTTCTTTCGAACAACCATTT
* * *
1434174 TTTTTCTTTCGAGCTACTA-TT
1 TTTTTCTTTCGAACAACCATTT
*
1434195 TTTTTCTTTC-ATTCAA-CATTT
1 TTTTTCTTTCGA-ACAACCATTT
1434216 TTTTTC
1 TTTTTC
1434222 GATGGAGAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.05
21 22 0.56
22 15 0.38
ACGTcount: A:0.16, C:0.21, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTTTCTTTCGAACAACCATTT
Found at i:1434196 original size:22 final size:21
Alignment explanation
Indices: 1434152--1434204 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
1434142 TTTTCCTCTC
*
1434152 TTTTTCTTTCGAACAACCCTTT
1 TTTTTCTTTCGAACAA-CCATT
* * *
1434174 TTTTTCTTTCGAGCTACTATT
1 TTTTTCTTTCGAACAACCATT
1434195 TTTTTCTTTC
1 TTTTTCTTTC
1434205 ATTCAACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.13, C:0.23, G:0.06, T:0.58
Consensus pattern (21 bp):
TTTTTCTTTCGAACAACCATT
Found at i:1441540 original size:18 final size:19
Alignment explanation
Indices: 1441517--1441555 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1441507 TTTAAGTAGT
*
1441517 AATAAAAACGATTAAA-TA
1 AATAAAAACAATTAAAGTA
*
1441535 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
1441554 AA
1 AA
1441556 AAATAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:1446000 original size:16 final size:16
Alignment explanation
Indices: 1445963--1446003 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1445953 CCATTAAAAA
**
1445963 GCCCTAAAAAATAGGG
1 GCCCTAAAAAATAAAG
*
1445979 GTCCTAAAAAATAAAG
1 GCCCTAAAAAATAAAG
1445995 GCCCTAAAA
1 GCCCTAAAA
1446004 TCGAGTATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.15
Consensus pattern (16 bp):
GCCCTAAAAAATAAAG
Found at i:1446007 original size:74 final size:73
Alignment explanation
Indices: 1445927--1446136 Score: 244
Period size: 74 Copynumber: 2.8 Consensus size: 73
1445917 AGGGGCTCCG
* * *
1445927 AAATCGAGTATATCTATTAGTTGTTCCCATTAAAAAGCCCTAAAAAATAGGGGTCCTAAAAAATA
1 AAATCGAGTATATCTATCAGTTGTTACCATTAAAAAGCCCTAAAAAATAGGGGTCCCAAAAAA-A
*
1445992 AAGG-CCCTA
65 AAGGTACC-A
* * *
1446001 AAATCGAGTATATCTATCGGTTGTTGCCATTAAAAAACCCTAAAAAATAAGGGG-CCCAAAAAAA
1 AAATCGAGTATATCTATCAGTTGTTACCATTAAAAAGCCCTAAAAAAT-AGGGGTCCCAAAAAAA
* *
1446065 AGGGTACCG
65 AAGGTACCA
* * ***
1446074 AAATCGAGTATATCTATCAGTTGTTACTATTAAGAAGTCAAAAAAAAATAGGGGTCCCAAAAA
1 AAATCGAGTATATCTATCAGTTGTTACCATTAAAAAG-CCCTAAAAAATAGGGGTCCCAAAAA
1446137 TAAGTTCGAA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
73 41 0.35
74 70 0.60
75 5 0.04
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (73 bp):
AAATCGAGTATATCTATCAGTTGTTACCATTAAAAAGCCCTAAAAAATAGGGGTCCCAAAAAAAA
AGGTACCA
Found at i:1447277 original size:36 final size:36
Alignment explanation
Indices: 1447230--1447302 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1447220 GAATAGAATC
1447230 AGCTTCCAGAAAAAGGAAGCAAAAATGCAGGGCAAT
1 AGCTTCCAGAAAAAGGAAGCAAAAATGCAGGGCAAT
1447266 AGCTTCCAGAAAAAGGAAGCAAAAATGCAGGGCAAT
1 AGCTTCCAGAAAAAGGAAGCAAAAATGCAGGGCAAT
1447302 A
1 A
1447303 CAAACCAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.48, C:0.16, G:0.25, T:0.11
Consensus pattern (36 bp):
AGCTTCCAGAAAAAGGAAGCAAAAATGCAGGGCAAT
Found at i:1448030 original size:17 final size:17
Alignment explanation
Indices: 1448008--1448048 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
1447998 ATGGTTTTTA
1448008 GAACCGGACCGGTTAGC
1 GAACCGGACCGGTTAGC
1448025 GAACCGGACCGGTTAGC
1 GAACCGGACCGGTTAGC
1448042 GAACCGG
1 GAACCGG
1448049 TTATGCTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.37, T:0.10
Consensus pattern (17 bp):
GAACCGGACCGGTTAGC
Found at i:1453297 original size:20 final size:20
Alignment explanation
Indices: 1453268--1453319 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1453258 CCAAAATAGA
* *
1453268 AGTAATTTGAAAGTTCAATT
1 AGTAAATTGAAAGCTCAATT
1453288 AGTAAATTGAAAGCTCAATT
1 AGTAAATTGAAAGCTCAATT
1453308 AGTAAATTGAAA
1 AGTAAATTGAAA
1453320 AATTAAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (20 bp):
AGTAAATTGAAAGCTCAATT
Found at i:1459232 original size:15 final size:14
Alignment explanation
Indices: 1459212--1459246 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
1459202 TGAAAAGATA
1459212 AACGAATATAAACG
1 AACGAATATAAACG
1459226 TAACGAATATAAACG
1 -AACGAATATAAACG
1459241 AACGAA
1 AACGAA
1459247 CCTAAAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
AACGAATATAAACG
Found at i:1465975 original size:81 final size:81
Alignment explanation
Indices: 1465835--1465992 Score: 271
Period size: 81 Copynumber: 2.0 Consensus size: 81
1465825 GTCTCTTGCA
* * *
1465835 CAACTGGCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
1 CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
1465900 CGAACCATTCTTGGTG
66 CGAACCATTCTTGGTG
* *
1465916 CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTTGCTCCGCCATTTCGTGTG
1 CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
1465981 CGAACCATTCTT
66 CGAACCATTCTT
1465993 TGTAACTCGC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (81 bp):
CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
CGAACCATTCTTGGTG
Found at i:1466167 original size:55 final size:55
Alignment explanation
Indices: 1466108--1466355 Score: 270
Period size: 55 Copynumber: 4.5 Consensus size: 55
1466098 TAGAATTAAC
1466108 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
* *** *
1466163 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGT---G-TAGCCAAAAGT
* ** * *
1466222 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAG-C-TAAGTT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAG-T
* * *
1466276 GATTGAGCACCTCTGTGCTTCAATCGAG-GACTGACACCTCTGTGCATCCAACTA-T
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGTAGCCAA-AAGT
* *
1466331 GACTGAGCACCTATGTGCTTCAATC
1 GATTGAGCACCTCTGTGCTTCAATC
1466356 TAAATTCTGG
Statistics
Matches: 160, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
53 3 0.02
54 40 0.25
55 69 0.43
56 1 0.01
57 1 0.01
58 1 0.01
59 45 0.28
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (55 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
Found at i:1466206 original size:27 final size:28
Alignment explanation
Indices: 1466111--1466376 Score: 110
Period size: 27 Copynumber: 9.5 Consensus size: 28
1466101 AATTAACGAT
*
1466111 TGAGCACCTCTGTGCTTCAATCGAGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* ** * *
1466139 TGA-CACCTCTGTG-TAGCCAAAAGTG-AT
1 TGAGCACCTCTGTGCT--TCAATCGAGAAC
1466166 TGAGCACCTCTGTGCTTCAATCGAGAAC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* *** *
1466194 TGA-CACCTCTGTGCAGTTAAAAAAAAATGAC
1 TGAGCACCTCTGTGC--TTCAATCGAGA--AC
** * *
1466225 TGAGCACCTCTGTGCTTCAGCCGGGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* * *
1466253 TGA-CACCTCTGTG-TAGCTAA--GTTG-AT
1 TGAGCACCTCTGTGCT-TC-AATCG-AGAAC
*
1466279 TGAGCACCTCTGTGCTTCAATCGAGGAC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* *
1466307 TGA-CACCTCTGTGCATCCAA-CTATG-AC
1 TGAGCACCTCTGTGC-TTCAATCGA-GAAC
* *
1466334 TGAGCACCTATGTGCTTCAATCTA-AATTC
1 TGAGCACCTCTGTGCTTCAATCGAGAA--C
1466363 TG-GCACCTCTGTGC
1 TGAGCACCTCTGTGC
1466377 ATTGGAATGA
Statistics
Matches: 176, Mismatches: 37, Indels: 50
0.67 0.14 0.19
Matches are distributed among these distances:
26 8 0.05
27 76 0.43
28 62 0.35
29 10 0.06
30 4 0.02
31 5 0.03
32 11 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (28 bp):
TGAGCACCTCTGTGCTTCAATCGAGAAC
Found at i:1466315 original size:113 final size:114
Alignment explanation
Indices: 1466111--1466321 Score: 354
Period size: 113 Copynumber: 1.9 Consensus size: 114
1466101 AATTAACGAT
*
1466111 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1466176 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
* * *
1466225 TGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAG-C-TAAGTTGATTGAGCACCT
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAG-TGATTGAGCACCT
*
1466288 CTGTGCTTCAATCGAGGACTGACACCTCTGTGCA
65 CTGTGCTTCAATCGAGAACTGACACCTCTGTGCA
1466322 TCCAACTATG
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 3 0.03
113 47 0.52
114 41 0.45
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (114 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
Found at i:1466402 original size:54 final size:53
Alignment explanation
Indices: 1466108--1466413 Score: 227
Period size: 54 Copynumber: 5.5 Consensus size: 53
1466098 TAGAATTAAC
* * * * *
1466108 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCTA-AACTGACACCTCTGTGCATCCAACA-T
* ** *
1466163 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCTA-AACTGACACCTCTGTGCA--T---CCAACAT
* ** ** * * * * **
1466222 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGTT
1 GATTGAGCACCTCTGTGCTTCAATC-TAAACTGACACCTCTGTGCATCCAACAT
* *
1466276 GATTGAGCACCTCTGTGCTTCAATCGAGGACTGACACCTCTGTGCATCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCTA-AACTGACACCTCTGTGCATCCAAC-AT
* * * ***
1466331 GACTGAGCACCTATGTGCTTCAATCTAAATTCTGGCACCTCTGTGCATTGGA-AT
1 GATTGAGCACCTCTGTGCTTCAATCTAAA--CTGACACCTCTGTGCATCCAACAT
*
1466385 GATTGAGCACCTCTGTGCTACAATCTAAA
1 GATTGAGCACCTCTGTGCTTCAATCTAAA
1466414 ATCAAGCACC
Statistics
Matches: 203, Mismatches: 38, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
53 1 0.00
54 72 0.35
55 69 0.34
56 17 0.08
59 39 0.19
60 5 0.02
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (53 bp):
GATTGAGCACCTCTGTGCTTCAATCTAAACTGACACCTCTGTGCATCCAACAT
Found at i:1468348 original size:29 final size:29
Alignment explanation
Indices: 1468306--1468362 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1468296 CTTCATGTAC
1468306 TCTTTTAGTTCTGATTCGCAGGTAAATTT
1 TCTTTTAGTTCTGATTCGCAGGTAAATTT
* *
1468335 TCTTTTA-TTGCTGATTCTCGGGTAAATT
1 TCTTTTAGTT-CTGATTCGCAGGTAAATT
1468363 ATATAGTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (29 bp):
TCTTTTAGTTCTGATTCGCAGGTAAATTT
Found at i:1468386 original size:93 final size:94
Alignment explanation
Indices: 1468218--1468425 Score: 325
Period size: 93 Copynumber: 2.2 Consensus size: 94
1468208 AGTTTTGTCC
*
1468218 GTTCTGATTCTCAGGTAAGTTTTCTTTTAGTTGTGATTTGAAGCGGTAAATTATATAGTCACATT
1 GTTCTGATTCTCAGGTAAATTTTCTTTTAGTTGTGATTT-AAGCGGTAAATTATATAGTCACATT
1468283 TGTAATGAAAAGCCTTCATGTACTCTTTTA
65 TGTAATGAAAAGCCTTCATGTACTCTTTTA
* *
1468313 GTTCTGATTCGCAGGTAAATTTTCTTTTA-TTGCTGATTCT-CG-GGTAAATTATATAGTCACAT
1 GTTCTGATTCTCAGGTAAATTTTCTTTTAGTTG-TGATT-TAAGCGGTAAATTATATAGTCACAT
1468375 TTGTAATGAAAAGCCTTCATGTACTCTTTTA
64 TTGTAATGAAAAGCCTTCATGTACTCTTTTA
*
1468406 GTT-TGATTCTCGGGTAAATT
1 GTTCTGATTCTCAGGTAAATT
1468426 ATATAGTCAC
Statistics
Matches: 106, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
92 15 0.14
93 54 0.51
94 4 0.04
95 32 0.30
96 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.43
Consensus pattern (94 bp):
GTTCTGATTCTCAGGTAAATTTTCTTTTAGTTGTGATTTAAGCGGTAAATTATATAGTCACATTT
GTAATGAAAAGCCTTCATGTACTCTTTTA
Found at i:1468435 original size:63 final size:63
Alignment explanation
Indices: 1468346--1468469 Score: 239
Period size: 63 Copynumber: 2.0 Consensus size: 63
1468336 CTTTTATTGC
1468346 TGATTCTCGGGTAAATTATATAGTCACATTTGTAATGAAAAGCCTTCATGTACTCTTTTAGTT
1 TGATTCTCGGGTAAATTATATAGTCACATTTGTAATGAAAAGCCTTCATGTACTCTTTTAGTT
*
1468409 TGATTCTCGGGTAAATTATATAGTCACATTTGTAATGAAAAGCCTTCATGTACTGTTTTAG
1 TGATTCTCGGGTAAATTATATAGTCACATTTGTAATGAAAAGCCTTCATGTACTCTTTTAG
1468470 GTGTTCCTCT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (63 bp):
TGATTCTCGGGTAAATTATATAGTCACATTTGTAATGAAAAGCCTTCATGTACTCTTTTAGTT
Found at i:1470355 original size:3 final size:3
Alignment explanation
Indices: 1470347--1470405 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
1470337 AGAAAGGAAA
1470347 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1470395 CTT CTT CTT CT
1 CTT CTT CTT CT
1470406 CTGTTAGAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:1470535 original size:77 final size:77
Alignment explanation
Indices: 1470383--1470602 Score: 324
Period size: 65 Copynumber: 3.0 Consensus size: 77
1470373 TCTTCTTCTT
*
1470383 CTTCTTCTTCTTCTTCTTCTTCTCTGTTAGAAAAGTC--TGTGACAGAGTTTCATGAATATATGT
1 CTTCTTCTTCTTCTTCTTCTTCTCTGTTAGAAAAGTCTTTGTGACAGAGATTCATGAATATATGT
1470446 TAAGCAAGGCAA
66 TAAGCAAGGCAA
1470458 CTTCTTCTTCTTCTTCTTCTTCTCTGTTAGAAAAGTCTTTGTGACAGAGATTCATGAATATATGT
1 CTTCTTCTTCTTCTTCTTCTTCTCTGTTAGAAAAGTCTTTGTGACAGAGATTCATGAATATATGT
1470523 TAAGCAAGGCAA
66 TAAGCAAGGCAA
*
1470535 ------------CTTCGTCTTCTCTGTTAGAAAAGTCTTTGTGACAGAGATTCATGAATATATGT
1 CTTCTTCTTCTTCTTCTTCTTCTCTGTTAGAAAAGTCTTTGTGACAGAGATTCATGAATATATGT
1470588 TAAGCAAGGCAA
66 TAAGCAAGGCAA
1470600 CTT
1 CTT
1470603 TTGTTCCTCA
Statistics
Matches: 138, Mismatches: 2, Indels: 17
0.88 0.01 0.11
Matches are distributed among these distances:
65 64 0.46
75 37 0.27
77 37 0.27
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (77 bp):
CTTCTTCTTCTTCTTCTTCTTCTCTGTTAGAAAAGTCTTTGTGACAGAGATTCATGAATATATGT
TAAGCAAGGCAA
Found at i:1472081 original size:99 final size:99
Alignment explanation
Indices: 1471888--1472084 Score: 351
Period size: 100 Copynumber: 2.0 Consensus size: 99
1471878 CTCAACACTC
*
1471888 TTCAACACATGCGAGGCCATGCACCAACATTCCCCTACTGCAAACTCTCCTACTAACAACATCCT
1 TTCAACACATGCGAGGCCATGCACCAACATTCCCCTACTGCAAACTCTCCCACTAACAACATCCT
1471953 TCAACACACCACCTTGTTTAAACACAAACTTATG
66 TCAACACACCACCTTGTTTAAACACAAACTTATG
*
1471987 TTCAACACATGCGAGGCCATGCACCAACATTCCCCCTACTGTAAACTCTCCCACTAACAACATCC
1 TTCAACACATGCGAGGCCATGCACCAACATT-CCCCTACTGCAAACTCTCCCACTAACAACATCC
*
1472052 TTCAACACACCACCTTGTTTCAACA-AAACTTAT
65 TTCAACACACCACCTTGTTTAAACACAAACTTAT
1472085 TCGACTCATT
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
99 39 0.41
100 55 0.59
ACGTcount: A:0.33, C:0.36, G:0.08, T:0.23
Consensus pattern (99 bp):
TTCAACACATGCGAGGCCATGCACCAACATTCCCCTACTGCAAACTCTCCCACTAACAACATCCT
TCAACACACCACCTTGTTTAAACACAAACTTATG
Found at i:1474109 original size:18 final size:19
Alignment explanation
Indices: 1474072--1474116 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1474062 AAGATTTAAT
*
1474072 TAAATAAAATAGATAATAA
1 TAAATAAAAGAGATAATAA
*
1474091 TAAATAAAAGGGA-AATAA
1 TAAATAAAAGAGATAATAA
1474109 TAAA-AAAA
1 TAAATAAAA
1474117 TAAATAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
19 11 0.46
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (19 bp):
TAAATAAAAGAGATAATAA
Found at i:1480349 original size:14 final size:13
Alignment explanation
Indices: 1480311--1480368 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
1480301 TTGACCCAAC
*
1480311 TGAGTCAACCCAT
1 TGAGTCAACTCAT
*
1480324 GCTGAGTTAACTCGAT
1 --TGAGTCAACTC-AT
*
1480340 TGAGTCAACTCAC
1 TGAGTCAACTCAT
*
1480353 CGAGTCAACTCAT
1 TGAGTCAACTCAT
1480366 TGA
1 TGA
1480369 CTGTTAACTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
13 14 0.40
14 10 0.29
15 9 0.26
16 2 0.06
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (13 bp):
TGAGTCAACTCAT
Found at i:1480385 original size:30 final size:30
Alignment explanation
Indices: 1480351--1480413 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1480341 GAGTCAACTC
*
1480351 ACCGAGTCAACTCATTGACTGTTAACTTTG
1 ACCGAGTCAACTCATTGACCGTTAACTTTG
* *
1480381 ACCGAGTCAACTCGTTGACCGTTGACTTTG
1 ACCGAGTCAACTCATTGACCGTTAACTTTG
1480411 ACC
1 ACC
1480414 AAAATTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (30 bp):
ACCGAGTCAACTCATTGACCGTTAACTTTG
Found at i:1482373 original size:24 final size:24
Alignment explanation
Indices: 1482345--1482453 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
1482335 GAATATTTTA
*
1482345 TCTGATTT-TCGATTTGAATTCTGT
1 TCTGATTTCT-GATCTGAATTCTGT
** * *
1482369 TCTGATACCTGACCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
1482393 TCTGATTTCTGATCTGGATTCTAT
1 TCTGATTTCTGATCTGAATTCTGT
*
1482417 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
1482441 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1482454 ATATCCGTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
24 69 0.99
25 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:1482408 original size:12 final size:12
Alignment explanation
Indices: 1482387--1482453 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 12
1482377 CTGACCTGGA
*
1482387 TTCTGTTCTGAT
1 TTCTGATCTGAT
1482399 TTCTGATCTGGA-
1 TTCTGATCT-GAT
1482411 TTCT-ATTCTGAT
1 TTCTGA-TCTGAT
* *
1482423 ATCTGATCTGAA
1 TTCTGATCTGAT
* *
1482435 TTCTGTTTTGAT
1 TTCTGATCTGAT
1482447 TTCTGAT
1 TTCTGAT
1482454 ATATCCGTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
11 3 0.07
12 37 0.86
13 3 0.07
ACGTcount: A:0.16, C:0.15, G:0.16, T:0.52
Consensus pattern (12 bp):
TTCTGATCTGAT
Found at i:1482414 original size:48 final size:48
Alignment explanation
Indices: 1482345--1482453 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
1482335 GAATATTTTA
* * *
1482345 TCTGATTT-TCGATTTGAATTCTGTTCTGATACCTGACCTGGATTCTGT
1 TCTGATTTCT-GATCTGAATTCTATTCTGATACCTGACCTGAATTCTGT
* * *
1482393 TCTGATTTCTGATCTGGATTCTATTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTATTCTGATACCTGACCTGAATTCTGT
*
1482441 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1482454 ATATCCGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTATTCTGATACCTGACCTGAATTCTGT
Found at i:1487726 original size:76 final size:76
Alignment explanation
Indices: 1487565--1487709 Score: 229
Period size: 76 Copynumber: 1.9 Consensus size: 76
1487555 ATTTTAAATA
*
1487565 TTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGATTTA
*
1487630 GGATATTATTT
66 AGATATTATTT
* * *
1487641 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATATGTTTT-AGTATTTTAATTAAGATTT
1487705 AAGAT
65 AAGAT
1487710 GTTTTAGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 5 0.08
76 58 0.92
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.59
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGATTTA
AGATATTATTT
Found at i:1488310 original size:12 final size:11
Alignment explanation
Indices: 1488292--1488321 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
1488282 AATTCAATTA
1488292 TTTTATTTATT
1 TTTTATTTATT
1488303 TGTTTATTTATT
1 T-TTTATTTATT
1488315 TTTTATT
1 TTTTATT
1488322 CTTTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:1488411 original size:20 final size:19
Alignment explanation
Indices: 1488372--1488420 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1488362 TACTATTTAA
*
1488372 TATTTTATTATTTCCCTTT
1 TATTTTATTATTTCCATTT
*
1488391 T-TATTTATTATTATCTATTT
1 TAT-TTTATTATT-TCCATTT
1488411 TATTTTATTA
1 TATTTTATTA
1488421 AATCTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 10 0.40
20 13 0.52
21 1 0.04
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTATTATTTCCATTT
Found at i:1491358 original size:5 final size:5
Alignment explanation
Indices: 1491350--1491401 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
1491340 ATATTTTTGT
* * *
1491350 TTTTA TTTTCA TTTTA TTTTTG TTTTA TTTCA TTTTA TTTTCG TTTTA
1 TTTTA TTTT-A TTTTA -TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA
1491398 TTTT
1 TTTT
1491402 CAGCGAACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 25 0.66
6 13 0.34
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:1491364 original size:11 final size:11
Alignment explanation
Indices: 1491350--1491403 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
1491340 ATATTTTTGT
1491350 TTTTATTTTCA
1 TTTTATTTTCA
**
1491361 TTTTATTTTTG
1 TTTTATTTTCA
1491372 TTTTA-TTTCA
1 TTTTATTTTCA
*
1491382 TTTTATTTTCG
1 TTTTATTTTCA
1491393 TTTTATTTTCA
1 TTTTATTTTCA
1491404 GCGAACTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
10 8 0.22
11 28 0.78
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:1491382 original size:21 final size:21
Alignment explanation
Indices: 1491332--1491400 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
1491322 GAGGTAACCC
* *
1491332 ATTTCGTTATATTTTTGTTTTT
1 ATTTCATTTTATTTTTG-TTTT
1491354 ATTTTCATTTTATTTTTGTTTT
1 A-TTTCATTTTATTTTTGTTTT
*
1491376 ATTTCATTTTATTTTCGTTTT
1 ATTTCATTTTATTTTTGTTTT
1491397 ATTT
1 ATTT
1491401 TCAGCGAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 23 0.53
22 6 0.14
23 14 0.33
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (21 bp):
ATTTCATTTTATTTTTGTTTT
Found at i:1493531 original size:76 final size:76
Alignment explanation
Indices: 1493428--1493624 Score: 333
Period size: 76 Copynumber: 2.6 Consensus size: 76
1493418 ATTTTAAATA
* *
1493428 TTATATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATATATTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTA
1493493 GGATATTATTT
66 GGATATTATTT
* * * *
1493504 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTATTATTTTAATTAAGTTTTA
1 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTA
1493569 GGATATTATTT
66 GGATATTATTT
1493580 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAG-TTTTA
1 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGATTTTA
1493625 ATTAGGATTT
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 5 0.04
76 109 0.96
ACGTcount: A:0.27, C:0.01, G:0.11, T:0.61
Consensus pattern (76 bp):
TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTA
GGATATTATTT
Found at i:1493599 original size:32 final size:32
Alignment explanation
Indices: 1493545--1493606 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
1493535 TTTAAATAGG
1493545 TTTTATTATTTTAATTAAGTTTTAGGATATTAT
1 TTTTATTATTTTAATTAAGTTTTAGG-TATTAT
*
1493578 TTTTA-TATTTTATATT-TGTTTTAGGTATT
1 TTTTATTATTTTA-ATTAAGTTTTAGGTATT
1493607 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.65
Consensus pattern (32 bp):
TTTTATTATTTTAATTAAGTTTTAGGTATTAT
Found at i:1494264 original size:18 final size:19
Alignment explanation
Indices: 1494229--1494266 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1494219 AGTTATTTTA
**
1494229 TTTATTTGTTTATTTAATT
1 TTTATTTGTTTAAATAATT
1494248 TTTATTT-TTTAAATAATT
1 TTTATTTGTTTAAATAATT
1494266 T
1 T
1494267 AAAACCCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTATTTGTTTAAATAATT
Found at i:1494327 original size:18 final size:20
Alignment explanation
Indices: 1494302--1494350 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
1494292 TTAATATTTA
1494302 TTATTTTATTATT-TCCT-TT
1 TTATTTTATTATTAT-CTATT
1494321 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCTATT
1494340 TTATTTTATTA
1 TTATTTTATTA
1494351 AATCTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.41
19 9 0.33
20 7 0.26
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTATTATTATCTATT
Found at i:1494803 original size:35 final size:35
Alignment explanation
Indices: 1494762--1494836 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
1494752 TTCATGTTCA
*
1494762 AAATTCCAAAACACTTCATTTACATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
* * * *
1494797 AAATTCCAAAATACTTTAATTACATTTTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
1494832 AAATT
1 AAATT
1494837 AAAGTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCC
Found at i:1495221 original size:3 final size:3
Alignment explanation
Indices: 1495213--1495270 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
1495203 ACATAATAGA
1495213 TAT TAT TAT TAT TAT 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
1495261 TAT TAT TAT T
1 TAT TAT TAT T
1495271 GCAATCATAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1502751 original size:3 final size:3
Alignment explanation
Indices: 1502743--1502787 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
1502733 TATACCCTTA
* *
1502743 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT AAA TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1502788 TAAAATCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1502767 original size:23 final size:23
Alignment explanation
Indices: 1502740--1502787 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1502730 AAATATACCC
* *
1502740 TTATATTATTATTATTATTATTA
1 TTATATTATAAATATTATTATTA
1502763 TTATATTATAAATATTATTATTA
1 TTATATTATAAATATTATTATTA
1502786 TT
1 TT
1502788 TAAAATCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATATTATAAATATTATTATTA
Found at i:1509731 original size:22 final size:22
Alignment explanation
Indices: 1509689--1509731 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1509679 TGATTTGGTC
*
1509689 TTATTCCAATTAAATGCATATT
1 TTATTCCAATTAAATGAATATT
*
1509711 TTATT-CATTTAAATGGAATAT
1 TTATTCCAATTAAAT-GAATAT
1509732 AATGTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (22 bp):
TTATTCCAATTAAATGAATATT
Found at i:1511443 original size:21 final size:21
Alignment explanation
Indices: 1511374--1511443 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
1511364 TAAACATGAA
1511374 AATAAGCTTACGAGCTTATGG
1 AATAAGCTTACGAGCTTATGG
* *
1511395 AATAA--TGACAAG-TATATTGG
1 AATAAGCTTACGAGCT-TA-TGG
1511415 TAAAATAAGCTTACGAGCTTATGG
1 ---AATAAGCTTACGAGCTTATGG
1511439 AATAA
1 AATAA
1511444 ATAGTAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
18 1 0.03
19 7 0.19
20 3 0.08
21 10 0.27
23 5 0.14
24 3 0.08
25 7 0.19
26 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (21 bp):
AATAAGCTTACGAGCTTATGG
Found at i:1511730 original size:45 final size:45
Alignment explanation
Indices: 1511372--1511729 Score: 538
Period size: 45 Copynumber: 8.0 Consensus size: 45
1511362 GGTAAACATG
**
1511372 AAAATAAGCTTACGAGCTTATGGAAT-AATGACAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
1511416 AAAATAAGCTTACGAGCTTATGGAATAAATAGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * * *
1511461 AAAATAAACTTACAAGCTTATAGAATAAATAGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
1511506 AAAATAAGCTTACGAGCTTTTGGAGTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
1511551 AAAATAAGCTTACGAGCTTATGGAATAAATAGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
1511596 AAAATAAGCTTATGAGCTTATGGAGTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * * *
1511641 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGAATTTTGGA
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * *
1511686 AAAATAAACTTACGAGTTTATAGAATAAATGGTAAGTATATTGG
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGG
1511730 ATATATTGGT
Statistics
Matches: 285, Mismatches: 28, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
44 26 0.09
45 259 0.91
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:1514297 original size:2 final size:2
Alignment explanation
Indices: 1514290--1514317 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1514280 GAACAAAAAG
1514290 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
1514318 TTCTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1530900 original size:24 final size:24
Alignment explanation
Indices: 1530867--1530925 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 24
1530857 CTCATATTGC
1530867 CATCACATTTCTACAATACGATCCA
1 CATC-CATTTCTACAATACGATCCA
*
1530892 CATCCATTTGTACAATACGATCCA
1 CATCCATTTCTACAATACGATCCA
1530916 CATCCATTTC
1 CATCCATTTC
1530926 ATTTTGCCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (24 bp):
CATCCATTTCTACAATACGATCCA
Found at i:1533958 original size:19 final size:20
Alignment explanation
Indices: 1533921--1533958 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1533911 AGAATAAAAT
* *
1533921 AAATATGGATGGTATTGTGG
1 AAATATGGATGGCAATGTGG
1533941 AAATAT-GATGGCAATGTG
1 AAATATGGATGGCAATGTG
1533959 AGATGTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.32
Consensus pattern (20 bp):
AAATATGGATGGCAATGTGG
Found at i:1537996 original size:16 final size:16
Alignment explanation
Indices: 1537975--1538007 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1537965 AAGGGCTATA
*
1537975 ACCATGCATGTCAAAC
1 ACCATGCATATCAAAC
1537991 ACCATGCATATCAAAC
1 ACCATGCATATCAAAC
1538007 A
1 A
1538008 TATCATACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.18
Consensus pattern (16 bp):
ACCATGCATATCAAAC
Found at i:1541161 original size:27 final size:27
Alignment explanation
Indices: 1541130--1541182 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1541120 GATCCAGGCG
1541130 GATTTCTCGGTCATGATCAGAGATCCA
1 GATTTCTCGGTCATGATCAGAGATCCA
1541157 GATTTCTCGGTCATGATCAGAGATCC
1 GATTTCTCGGTCATGATCAGAGATCC
1541183 CATGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (27 bp):
GATTTCTCGGTCATGATCAGAGATCCA
Found at i:1542875 original size:12 final size:12
Alignment explanation
Indices: 1542858--1542887 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1542848 CTAATGCTTG
1542858 AAAATAATAATA
1 AAAATAATAATA
1542870 AAAATAATAATA
1 AAAATAATAATA
*
1542882 ACAATA
1 AAAATA
1542888 TTATCCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:1547118 original size:11 final size:11
Alignment explanation
Indices: 1547102--1547129 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1547092 AAACAAGTGC
1547102 TTAATTATAAA
1 TTAATTATAAA
1547113 TTAATTATAAA
1 TTAATTATAAA
1547124 TTAATT
1 TTAATT
1547130 TATTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTAATTATAAA
Found at i:1553727 original size:11 final size:11
Alignment explanation
Indices: 1553711--1553735 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1553701 ATACAAGTTC
1553711 TTAATTATAAA
1 TTAATTATAAA
1553722 TTAATTATAAA
1 TTAATTATAAA
1553733 TTA
1 TTA
1553736 CTTTATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATTATAAA
Found at i:1555488 original size:18 final size:18
Alignment explanation
Indices: 1555455--1555490 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1555445 TAAATTTTAT
* *
1555455 AAGTATCAAGTTGAAATA
1 AAGTATCAAATAGAAATA
1555473 AAGTATCAAATAGAAATA
1 AAGTATCAAATAGAAATA
1555491 GTAAATGAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.25
Consensus pattern (18 bp):
AAGTATCAAATAGAAATA
Done.