Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005071.1 Hibiscus syriacus cultivar Beakdansim tig00011384_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: 85813
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:480 original size:15 final size:16
Alignment explanation
Indices: 447--481 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
437 CATTAGGATT
447 TATCTTTTCATGATTAA
1 TATCTTTTCATGA-TAA
464 TATCTTTTCATGA-AA
1 TATCTTTTCATGATAA
479 TAT
1 TAT
482 TTAAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
17 13 0.72
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (16 bp):
TATCTTTTCATGATAA
Found at i:3397 original size:15 final size:16
Alignment explanation
Indices: 3367--3399 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3357 GAATCATTAG
3367 GATTAATATCTTTCAT
1 GATTAATATCTTTCAT
*
3383 GATTAATCT-TTTCAT
1 GATTAATATCTTTCAT
3398 GA
1 GA
3400 AATATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (16 bp):
GATTAATATCTTTCAT
Found at i:3728 original size:20 final size:18
Alignment explanation
Indices: 3693--3730 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3683 TTCTCCTCAT
3693 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
3711 TTCCTCCATCTTTT-TTC
1 TTCCTCCATCTTTTCTTC
3728 TTC
1 TTC
3731 AAATTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.58
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:4095 original size:15 final size:15
Alignment explanation
Indices: 4075--4104 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4065 ACTATGTTTT
4075 CCCTGACCGTAATCC
1 CCCTGACCGTAATCC
*
4090 CCCTGACCGTCATCC
1 CCCTGACCGTAATCC
4105 ACCCCTCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.50, G:0.13, T:0.20
Consensus pattern (15 bp):
CCCTGACCGTAATCC
Found at i:4144 original size:9 final size:9
Alignment explanation
Indices: 4130--4163 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
4120 CTTCTTCCCT
4130 CTCCTCTGC
1 CTCCTCTGC
4139 CTCCTCTGC
1 CTCCTCTGC
*
4148 CTTCTCTGC
1 CTCCTCTGC
4157 CTCCTCT
1 CTCCTCT
4164 ACGTCCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.53, G:0.09, T:0.38
Consensus pattern (9 bp):
CTCCTCTGC
Found at i:5785 original size:16 final size:16
Alignment explanation
Indices: 5764--5795 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5754 ACCTCCCTAT
5764 TTCCTTCAATGAATGG
1 TTCCTTCAATGAATGG
5780 TTCCTTCAATGAATGG
1 TTCCTTCAATGAATGG
5796 AACACTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
TTCCTTCAATGAATGG
Found at i:6358 original size:20 final size:20
Alignment explanation
Indices: 6312--6358 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
6302 ACTGGTAGCG
6312 CTTTACCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
6332 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
6353 -TTTACC
1 CTTTACC
6359 TATTATATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:6630 original size:181 final size:182
Alignment explanation
Indices: 6286--7646 Score: 2080
Period size: 181 Copynumber: 7.6 Consensus size: 182
6276 ATTAAAGTAC
* * * ** * * *
6286 CGACACTTTCAACATAACTGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * * **
6351 TTTTTACCTATTATATTGTTATGGATCGATACATTT-TCATAAAGTATCGATGCTTTTTAGGCGC
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGT-ATAAAGTATCGACACTTTTTAGGCGC
* **
6415 TATAATTTCTTCTC-TTTAAATTATGAAAGTGTCGATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
*
6467 CGACACTTTCAATATATCCGGTAACTTTTTACCGGTTTTATCATTTCGAGACCTG-TTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
*
6531 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAATATCGACACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
* *
6596 ATAACTGCTTCTCTTTTAAATATA-AAAAGTGTCGATAATTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAAT-TACAAAAGTGTCGATACTTATATTAATTTAT
6648 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * *
6713 TTATTACATGTTATA-TGCTATGGATCGATATATTTGTATAAAGTATCGACACTTTTTAGGCTCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
6777 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* *
6829 CGACACTTTCAATATATCCGGTATCTTTTTACCGGTTTTATCATTTCGATACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
*
6894 TTATTACCTGTTATA-TGCTATGGATCGATACA-TTGTATAAAGTATCGATACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
6957 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
7009 CGACACTTTCAATATATCCGGTATG-TTTTTA-CGGTTTTATCATTTCGAGACCTGTTTTGTCAT
1 CGACACTTTCAATATATCCGGTA-GCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCAT
* *
7072 ATTATTACCTGTTATATTG--ATGGATCGATACATTTGTATAAA-TATCAACAATTTTTAGGCGC
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGC
7134 TATAACTTCTTCTCTTTTAAA-TATCAAAAGTGTCGATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTA-CAAAAGTGTCGATACTTATATTAATTTAT
*
7187 CGACACTTTCAATATATCCGATAGCTTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCAT
1 CGACACTTTCAATATATCCGGTAGC-TTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCAT
* *
7252 ATTATTACCTGTTATATTGCTATGGATTGATACA-TTGTATAAAGTATTGACACTTTTTAGGCGC
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGC
7316 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
** * * * *
7369 C-ACACTTTCAATATATCCGGTAGCGGTTTACCGG-TTTATCATAAT-GACACCGGTTTTGTCAC
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGAGACCTGTTTTGTCAT
* *
7431 ATTATTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTATAGGCGC
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGC
7496 TATAACTTC-T-TCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
** * * * * *
7547 CGACACTTTCAATATATCCGGTAGCGGTTTACCGATTTTATCATAAT-GACACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGAGACCTGTTTTGTCAT
* *
7611 ATTTTTA-CTGTTATATTTCTATGGATCGATACATTT
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTT
7647 TCATTTGTAT
Statistics
Matches: 1102, Mismatches: 58, Indels: 42
0.92 0.05 0.03
Matches are distributed among these distances:
177 3 0.00
178 144 0.13
179 177 0.16
180 320 0.29
181 351 0.32
182 105 0.10
183 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
Found at i:7316 original size:360 final size:362
Alignment explanation
Indices: 6286--7645 Score: 2072
Period size: 360 Copynumber: 3.8 Consensus size: 362
6276 ATTAAAGTAC
* * * ** * *
6286 CGACACTTTCAACATAACTGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * **
6351 TTTTTACCTATTATATTGTTATGGATCGATACATTT-TCATAAAGTATCGATGCTTTTTAGGCGC
66 TTATTACCTGTTATATTG-TATGGATCGATACATTTGT-ATAAAGTATCGACACTTTTTAGGCGC
* **
6415 TATAATTTCTTCTC-TTTAAATTATGAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAA
129 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAA
*
6479 TATATCCGGTAACTTTTTACCGGTTTTATCATTTCGAGACCTG-TTTGTCATATTATTACCTGTT
194 TATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGTT
* *
6543 ATATTGCTATGGATCGATACATTTGTATAAAATATCGACACTTTTTAGGCGCTATAACTGCTTCT
259 ATATTGCTATGGATCGATACA-TTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCT
*
6608 CTTTTAAATATA-AAAAGTGTCGATAATTATATTAATTTAT
323 CTTTTAAAT-TACAAAAGTGTCGATACTTATATTAATTTAT
*
6648 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * *
6713 TTATTACATGTTATA-TGCTATGGATCGATATATTTGTATAAAGTATCGACACTTTTTAGGCTCT
66 TTATTACCTGTTATATTG-TATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
6777 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAAT
130 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAAT
* *
6842 ATATCCGGTATCTTTTTACCGGTTTTATCATTTCGATACCTGTTTTGTCATATTATTACCTGTTA
195 ATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGTTA
*
6907 TA-TGCTATGGATCGATACATTGTATAAAGTATCGATACTTTTTAGGCGCTATAACTTCTTCTCT
260 TATTGCTATGGATCGATACATTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCT
6971 TTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
325 TTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
*
7009 CGACACTTTCAATATATCCGGTATG-TTTTTA-CGGTTTTATCATTTCGAGACCTGTTTTGTCAT
1 CGACACTTTCAATATATCCGGTA-GCTTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCAT
* *
7072 ATTATTACCTGTTATATTG-ATGGATCGATACATTTGTATAAA-TATCAACAATTTTTAGGCGCT
65 ATTATTACCTGTTATATTGTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
7135 ATAACTTCTTCTCTTTTAAA-TATCAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAA
130 ATAACTTCTTCTCTTTTAAATTA-CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAA
*
7199 TATATCCGATAGCTTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGT
194 TATATCCGGTAGC-TTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGT
* *
7264 TATATTGCTATGGATTGATACATTGTATAAAGTATTGACACTTTTTAGGCGCTATAACTTCTTCT
258 TATATTGCTATGGATCGATACATTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCT
7329 CTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
323 CTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
** * * *
7369 C-ACACTTTCAATATATCCGGTAGCGGTTTACCGG-TTTATCATAAT-GACACCGGTTTTGTCAC
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGAGACCGGTTTTGTCAT
* *
7431 ATTATTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTATAGGCGC
65 ATTATTACCTGTTATATT-GTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGC
7496 TATAACTTC-T-TCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAA
129 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAA
** * * * * * *
7559 TATATCCGGTAGCGGTTTACCGATTTTATCATAAT-GACACCGGTTTTATCATATTTTTA-CTGT
194 TATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGAGACCTGTTTTGTCATATTATTACCTGT
*
7622 TATATTTCTATGGATCGATACATT
258 TATATTGCTATGGATCGATACATT
7646 TTCATTTGTA
Statistics
Matches: 924, Mismatches: 57, Indels: 38
0.91 0.06 0.04
Matches are distributed among these distances:
357 2 0.00
358 117 0.13
359 177 0.19
360 214 0.23
361 187 0.20
362 203 0.22
363 24 0.03
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (362 bp):
CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
TTATTACCTGTTATATTGTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTA
TAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATA
TATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGTTAT
ATTGCTATGGATCGATACATTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTT
TTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
Found at i:9907 original size:52 final size:53
Alignment explanation
Indices: 9817--9921 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 53
9807 TAATAATCCT
9817 CACATATATATTCACAAAGCGATCAAAGTGATAGATGATATGACCAAAATGGC
1 CACATATATATTCACAAAGCGATCAAAGTGATAGATGATATGACCAAAATGGC
*
9870 CACATATATATTCACAAAG-GATCAAAGTGATAGATGATATGACTAAAATGGC
1 CACATATATATTCACAAAGCGATCAAAGTGATAGATGATATGACCAAAATGGC
9922 ATGGGATCTC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 32 0.63
53 19 0.37
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (53 bp):
CACATATATATTCACAAAGCGATCAAAGTGATAGATGATATGACCAAAATGGC
Found at i:10782 original size:22 final size:22
Alignment explanation
Indices: 10757--10798 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
10747 ATTAATACTA
10757 TAAAATAAGAGTCTTTTTAACC
1 TAAAATAAGAGTCTTTTTAACC
*
10779 TAAAATAGGAGTCTTTTTAA
1 TAAAATAAGAGTCTTTTTAA
10799 ATTAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
TAAAATAAGAGTCTTTTTAACC
Found at i:10804 original size:22 final size:22
Alignment explanation
Indices: 10757--10806 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
10747 ATTAATACTA
*
10757 TAAAATAAGAGTCTTTTTAACC
1 TAAAATAAGAGTCTTTTTAAAC
* *
10779 TAAAATAGGAGTCTTTTTAAAT
1 TAAAATAAGAGTCTTTTTAAAC
10801 TAAAAT
1 TAAAAT
10807 GAAATGTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (22 bp):
TAAAATAAGAGTCTTTTTAAAC
Found at i:16104 original size:3 final size:3
Alignment explanation
Indices: 16083--16139 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
16073 AAATATGTAA
*
16083 AAT AAT ATT AAT -AT CAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
16128 AAT -TT AAT AAT A
1 AAT AAT AAT AAT A
16140 TTTTTAACCC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 3 0.06
3 42 0.89
4 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:29401 original size:15 final size:15
Alignment explanation
Indices: 29376--29411 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
29366 GTAGACCAAT
29376 TTTTGTCTTAAAATTA
1 TTTT-TCTTAAAATTA
29392 TTTTTCTTAAAATTA
1 TTTTTCTTAAAATTA
29407 TTTTT
1 TTTTT
29412 AAAAGACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTTTCTTAAAATTA
Found at i:33491 original size:7 final size:7
Alignment explanation
Indices: 33479--33505 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
33469 TGAAACTATA
33479 TAACATG
1 TAACATG
33486 TAACATG
1 TAACATG
33493 TAACATG
1 TAACATG
33500 TAACAT
1 TAACAT
33506 ACTAACTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (7 bp):
TAACATG
Found at i:34678 original size:215 final size:215
Alignment explanation
Indices: 34422--34816 Score: 592
Period size: 215 Copynumber: 1.8 Consensus size: 215
34412 TTTGTGATAG
* * *
34422 AATCGAACAAGATAAAATTACGTTGATTCAACTCCTTTTGTGAAGAATCGAACGGAATGACACTA
1 AATCGAAAAAGATAAAATTACGTTGATTCAACTCATTTTGTGAAGAATCGAACGAAATGACACTA
* * * * *
34487 TTGACCAAAATCCTTCTGTGGAGAATCAATCAAAATGTCGAAGTTGTTATATCTCATTCTGTGAT
66 TTGACCAAAATCCATATGTGGAGAATCAAACAAAATGTCGAAGTTGATATACCTCATTCTGTGAT
* * *
34552 AGAATCGAGCAAGATGAAATTACGCTGATCCAACTCCTTCTGTGAAGAATTAAGCAAAAGGTTGG
131 AGAATCAAACAAAATGAAATTACGCTGATCCAACTCCTTCTGTGAAGAATTAAGCAAAAGGTTGG
34617 TACTTATCCATCTTTGATGA
196 TACTTATCCATCTTTGATGA
* *
34637 AATCGAAAAAGATAAAATTACGTTGATTCAACTCATTTTGTGAAGAATCGATCGAAATGATACTA
1 AATCGAAAAAGATAAAATTACGTTGATTCAACTCATTTTGTGAAGAATCGAACGAAATGACACTA
* * * * *
34702 TTGACCTAATTCCATATGTGGAGGATCAAACAAAATGTCGATGTTGATCTACCTCATTCTGTGAT
66 TTGACCAAAATCCATATGTGGAGAATCAAACAAAATGTCGAAGTTGATATACCTCATTCTGTGAT
* ** *
34767 AGAATTAAACAAAATGATGTTATGCTGATCCAACTCCTTCTGTGAAGAAT
131 AGAATCAAACAAAATGAAATTACGCTGATCCAACTCCTTCTGTGAAGAAT
34817 CGAACAAAAT
Statistics
Matches: 158, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
215 158 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (215 bp):
AATCGAAAAAGATAAAATTACGTTGATTCAACTCATTTTGTGAAGAATCGAACGAAATGACACTA
TTGACCAAAATCCATATGTGGAGAATCAAACAAAATGTCGAAGTTGATATACCTCATTCTGTGAT
AGAATCAAACAAAATGAAATTACGCTGATCCAACTCCTTCTGTGAAGAATTAAGCAAAAGGTTGG
TACTTATCCATCTTTGATGA
Found at i:34808 original size:46 final size:44
Alignment explanation
Indices: 34726--34863 Score: 118
Period size: 44 Copynumber: 3.1 Consensus size: 44
34716 TATGTGGAGG
* * * * * * *
34726 ATCAAACAAAATGTCGATGTTGATCTACCTCATTCTGTGATAGA
1 ATCAAACAAAATATTGGTATTGATCCAACTCCTTCTGTGATAGA
* *
34770 ATTAAACAAAATGA-TGTTATGCTGATCCAACTCCTTCTGTGA-AGA
1 ATCAAACAAAAT-ATTGGTAT--TGATCCAACTCCTTCTGTGATAGA
* * * *
34815 ATCGAACAAAATATTGGTATTGATCCATCTCTTTCTGTGATAAA
1 ATCAAACAAAATATTGGTATTGATCCAACTCCTTCTGTGATAGA
34859 ATCAA
1 ATCAA
34864 GCACCGAAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
43 18 0.24
44 21 0.28
45 18 0.24
46 17 0.23
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (44 bp):
ATCAAACAAAATATTGGTATTGATCCAACTCCTTCTGTGATAGA
Found at i:35361 original size:1 final size:1
Alignment explanation
Indices: 35351--35395 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
35341 TTCCACTTTA
* * * *
35351 TTTTTCTTTTTTTCTTTTTTTTTCTTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35396 CTCTTTTGCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:35370 original size:10 final size:10
Alignment explanation
Indices: 35357--35394 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
35347 TTTATTTTTC
35357 TTTTTTTCTT
1 TTTTTTTCTT
35367 TTTTTTTCTTT
1 TTTTTTTC-TT
35378 TTTTTTTCTT
1 TTTTTTTCTT
35388 TTTTTTT
1 TTTTTTT
35395 TCTCTTTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:35372 original size:18 final size:18
Alignment explanation
Indices: 35346--35402 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
35336 CAGACTTCCA
*
35346 CTTTATTTTTCTTTTTTT
1 CTTTTTTTTTCTTTTTTT
35364 CTTTTTTTTTCTTTTTTT
1 CTTTTTTTTTCTTTTTTT
* *
35382 -TTTCTTTTT-TTTTTCT
1 CTTTTTTTTTCTTTTTTT
35398 CTTTT
1 CTTTT
35403 GCAACTGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 6 0.18
17 11 0.32
18 17 0.50
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (18 bp):
CTTTTTTTTTCTTTTTTT
Found at i:35373 original size:11 final size:11
Alignment explanation
Indices: 35357--35402 Score: 76
Period size: 11 Copynumber: 4.2 Consensus size: 11
35347 TTTATTTTTC
35357 TTTTTTTC-TT
1 TTTTTTTCTTT
35367 TTTTTTTCTTT
1 TTTTTTTCTTT
35378 TTTTTTTCTTT
1 TTTTTTTCTTT
35389 TTTTTTTCTCTT
1 TTTTTTTCT-TT
35401 TT
1 TT
35403 GCAACTGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 8 0.24
11 22 0.65
12 4 0.12
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:35402 original size:10 final size:10
Alignment explanation
Indices: 35346--35392 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
35336 CAGACTTCCA
35346 CTTTATTTT-T
1 CTTT-TTTTCT
35356 CTTTTTTTCT
1 CTTTTTTTCT
*
35366 TTTTTTTTCT
1 CTTTTTTTCT
*
35376 -TTTTTTTTT
1 CTTTTTTTCT
35385 CTTTTTTT
1 CTTTTTTT
35393 TTTCTCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 12 0.36
10 21 0.64
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:36057 original size:7 final size:7
Alignment explanation
Indices: 36034--36086 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
36024 TGAACCCTCC
36034 TTTTCTT
1 TTTTCTT
*
36041 TTTT-TA
1 TTTTCTT
36047 TTTTCTT
1 TTTTCTT
36054 TTTTCTT
1 TTTTCTT
*
36061 TTTGCTCT
1 TTTTCT-T
**
36069 TTTTGAT
1 TTTTCTT
36076 TTTTCTT
1 TTTTCTT
36083 TTTT
1 TTTT
36087 TTCTTCAAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
6 5 0.14
7 27 0.75
8 4 0.11
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:38430 original size:15 final size:15
Alignment explanation
Indices: 38410--38443 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38400 AACCTTACCC
*
38410 GCCCCGCATCTGCCT
1 GCCCCGCATCCGCCT
*
38425 GCCCCGTATCCGCCT
1 GCCCCGCATCCGCCT
38440 GCCC
1 GCCC
38444 ACTAAATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.56, G:0.21, T:0.18
Consensus pattern (15 bp):
GCCCCGCATCCGCCT
Found at i:42954 original size:2 final size:2
Alignment explanation
Indices: 42947--42979 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42937 TTTTTAAAAC
42947 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
42980 CCCCCATCCC
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:43173 original size:24 final size:24
Alignment explanation
Indices: 43146--43245 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
43136 GATATCAAAA
*
43146 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
43170 ATCATAACAGAATCCA-AGTTAGGA-
1 ATCAAAACAGAATTCAGA-TCA-GAT
* *
43194 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
43218 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
43242 ATCA
1 ATCA
43246 GATAAAATAT
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
23 3 0.05
24 52 0.90
25 3 0.05
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:43245 original size:48 final size:48
Alignment explanation
Indices: 43139--43247 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
43129 AAACGGAGAT
* * * *
43139 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
43187 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
43235 ATCAGAAATCAGA
1 ATCAGAAATCAGA
43248 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:44406 original size:18 final size:18
Alignment explanation
Indices: 44385--44420 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44375 CTTCCATCCG
*
44385 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
44403 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
44421 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:45743 original size:8 final size:8
Alignment explanation
Indices: 45730--45769 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
45720 GGTCAACTCC
45730 GGTCAACG
1 GGTCAACG
45738 GGTCAAC-
1 GGTCAACG
45745 GGTCAACG
1 GGTCAACG
45753 GGT---CG
1 GGTCAACG
45758 GGTCAACG
1 GGTCAACG
45766 GGTC
1 GGTC
45770 GGTTCGGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:45749 original size:15 final size:13
Alignment explanation
Indices: 45727--45769 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
45717 AGTGGTCAAC
45727 TCCGGTCAACGGG
1 TCCGGTCAACGGG
45740 TCAACGGTCAACGGG
1 TC--CGGTCAACGGG
*
45755 TCGGGTCAACGGG
1 TCCGGTCAACGGG
45768 TC
1 TC
45770 GGTTCGGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 14 0.52
15 13 0.48
ACGTcount: A:0.19, C:0.28, G:0.37, T:0.16
Consensus pattern (13 bp):
TCCGGTCAACGGG
Found at i:45778 original size:18 final size:18
Alignment explanation
Indices: 45751--45795 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
45741 CAACGGTCAA
*
45751 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
45769 CGGTTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
45787 CGGGTCGGG
1 CGGGTCGGG
45796 CTGTGACCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.20, G:0.51, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:47747 original size:2 final size:2
Alignment explanation
Indices: 47740--47772 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
47730 TTTTTAAAAC
47740 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
47773 CCCCCATCCC
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:47966 original size:24 final size:24
Alignment explanation
Indices: 47939--48038 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
47929 GATATCAAAA
*
47939 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
47963 ATCATAACAGAATCCA-AGTTAGGA-
1 ATCAAAACAGAATTCAGA-TCA-GAT
* *
47987 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
48011 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
48035 ATCA
1 ATCA
48039 GATAAAATAT
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
23 3 0.05
24 52 0.90
25 3 0.05
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:48038 original size:48 final size:48
Alignment explanation
Indices: 47932--48040 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
47922 AAACGGAGAT
* * * *
47932 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
47980 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
48028 ATCAGAAATCAGA
1 ATCAGAAATCAGA
48041 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:49200 original size:18 final size:18
Alignment explanation
Indices: 49179--49214 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
49169 CTTCCATCCG
*
49179 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
49197 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
49215 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:50537 original size:8 final size:8
Alignment explanation
Indices: 50524--50563 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
50514 GGTCAACTCC
50524 GGTCAACG
1 GGTCAACG
50532 GGTCAAC-
1 GGTCAACG
50539 GGTCAACG
1 GGTCAACG
50547 GGT---CG
1 GGTCAACG
50552 GGTCAACG
1 GGTCAACG
50560 GGTC
1 GGTC
50564 GGTTCGGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:50543 original size:15 final size:13
Alignment explanation
Indices: 50521--50563 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
50511 AGTGGTCAAC
50521 TCCGGTCAACGGG
1 TCCGGTCAACGGG
50534 TCAACGGTCAACGGG
1 TC--CGGTCAACGGG
*
50549 TCGGGTCAACGGG
1 TCCGGTCAACGGG
50562 TC
1 TC
50564 GGTTCGGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 14 0.52
15 13 0.48
ACGTcount: A:0.19, C:0.28, G:0.37, T:0.16
Consensus pattern (13 bp):
TCCGGTCAACGGG
Found at i:50572 original size:18 final size:18
Alignment explanation
Indices: 50545--50589 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
50535 CAACGGTCAA
*
50545 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
50563 CGGTTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
50581 CGGGTCGGG
1 CGGGTCGGG
50590 CTGTGACCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.20, G:0.51, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:53211 original size:18 final size:20
Alignment explanation
Indices: 53171--53215 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
53161 TAGTATCGTC
*
53171 ATAGTAATAAGTAAAATACA
1 ATAGTAATAACTAAAATACA
53191 ATAGTAATAACT-AAA-ACA
1 ATAGTAATAACTAAAATACA
53209 ATAGTAA
1 ATAGTAA
53216 AACCTAGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.42
19 3 0.12
20 11 0.46
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (20 bp):
ATAGTAATAACTAAAATACA
Found at i:57356 original size:21 final size:21
Alignment explanation
Indices: 57320--57374 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
57310 AACCTTACCC
* *
57320 AATCAAAAAAGATTTGTGACA
1 AATCCAAAAAGGTTTGTGACA
*
57341 AATCCAACAAGGTTTGTGACA
1 AATCCAAAAAGGTTTGTGACA
57362 AATCCAAAAAGGT
1 AATCCAAAAAGGT
57375 ATGGGGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (21 bp):
AATCCAAAAAGGTTTGTGACA
Found at i:65141 original size:20 final size:20
Alignment explanation
Indices: 65116--65153 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
65106 TTTGGTTCAC
65116 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
65136 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
65154 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:68933 original size:22 final size:19
Alignment explanation
Indices: 68908--68951 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
68898 ATGGGGTTTG
68908 AAAGAAGAAAAGGAAAATAACA
1 AAAGAAG-AAAGG--AATAACA
*
68930 AAAGAAGCAAGGAATAACA
1 AAAGAAGAAAGGAATAACA
68949 AAA
1 AAA
68952 CCATGAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
21 4 0.19
22 7 0.33
ACGTcount: A:0.70, C:0.07, G:0.18, T:0.05
Consensus pattern (19 bp):
AAAGAAGAAAGGAATAACA
Found at i:71573 original size:6 final size:6
Alignment explanation
Indices: 71556--71624 Score: 85
Period size: 6 Copynumber: 12.0 Consensus size: 6
71546 CTCGATCAAG
71556 GCTCGA -CTCGA GCTCGA GCTCG- GACTCGA -CTCGA GCTCGA GCTCG-
1 GCTCGA GCTCGA GCTCGA GCTCGA G-CTCGA GCTCGA GCTCGA GCTCGA
71601 GACTCGA -CTCGA GCTCGA GCTCGA
1 G-CTCGA GCTCGA GCTCGA GCTCGA
71625 CTTGAGTTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
5 17 0.30
6 39 0.70
ACGTcount: A:0.17, C:0.35, G:0.30, T:0.17
Consensus pattern (6 bp):
GCTCGA
Found at i:71584 original size:23 final size:23
Alignment explanation
Indices: 71557--71623 Score: 134
Period size: 23 Copynumber: 2.9 Consensus size: 23
71547 TCGATCAAGG
71557 CTCGACTCGAGCTCGAGCTCGGA
1 CTCGACTCGAGCTCGAGCTCGGA
71580 CTCGACTCGAGCTCGAGCTCGGA
1 CTCGACTCGAGCTCGAGCTCGGA
71603 CTCGACTCGAGCTCGAGCTCG
1 CTCGACTCGAGCTCGAGCTCG
71624 ACTTGAGTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.16, C:0.36, G:0.30, T:0.18
Consensus pattern (23 bp):
CTCGACTCGAGCTCGAGCTCGGA
Found at i:71588 original size:17 final size:16
Alignment explanation
Indices: 71534--71624 Score: 87
Period size: 17 Copynumber: 5.4 Consensus size: 16
71524 ATCGCGAGCT
*
71534 ACTCGAGATCGACTCG
1 ACTCGAGCTCGACTCG
*
71550 A-TCAAGGCTCGACTCG
1 ACTCGA-GCTCGACTCG
71566 AGCTCGAGCTCGGACTCG
1 A-CTCGAGCTC-GACTCG
71584 ACTCGAGCTCGAGCTCGG
1 ACTCGAGCTCGA-CTC-G
71602 ACTCGA-CTCGAGCTCG
1 ACTCGAGCTCGA-CTCG
71618 AGCTCGA
1 A-CTCGA
71625 CTTGAGTTCT
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
15 3 0.05
16 15 0.23
17 30 0.46
18 17 0.26
ACGTcount: A:0.21, C:0.33, G:0.29, T:0.18
Consensus pattern (16 bp):
ACTCGAGCTCGACTCG
Found at i:72120 original size:25 final size:26
Alignment explanation
Indices: 72092--72146 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
72082 TTAATAAAAA
72092 AATAT-TTATCTAATGACAA-ATATTT
1 AATATATT-TCTAATGACAATATATTT
* *
72117 AATATATTTCTAATGATAATATTTTT
1 AATATATTTCTAATGACAATATATTT
72143 AATA
1 AATA
72147 ACTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (26 bp):
AATATATTTCTAATGACAATATATTT
Found at i:72319 original size:21 final size:21
Alignment explanation
Indices: 72295--72341 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
72285 TTGTAATGAA
*
72295 CCCTAAACCATAATTCTTAAT
1 CCCTAAACCATAATCCTTAAT
* *
72316 CCCTAAACCCTAATCCTTGAT
1 CCCTAAACCATAATCCTTAAT
72337 CCCTA
1 CCCTA
72342 CGTCCTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (21 bp):
CCCTAAACCATAATCCTTAAT
Found at i:73775 original size:16 final size:15
Alignment explanation
Indices: 73755--73783 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
73745 TTGAAGTTTT
73755 TTTTTTGAGTTTAAA
1 TTTTTTGAGTTTAAA
73770 TTTTTTGAGTTTAA
1 TTTTTTGAGTTTAA
73784 GTTGAGTTTT
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:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (15 bp):
TTTTTTGAGTTTAAA
Found at i:73838 original size:48 final size:46
Alignment explanation
Indices: 73787--73929 Score: 113
Period size: 48 Copynumber: 3.1 Consensus size: 46
73777 AGTTTAAGTT
* *
73787 GAGTTTTAATATTATTTTTTGAGTTTGAGGTTTTCGAGTTTTCGAGTT
1 GAGTTTTAATATTA-TTTTAGAGTTTGAGGTTTT-GAGTTTTCGAGTC
* *
73835 GAG-TTTACAT-TTA----AGAGTTTAAGCCTTTTTGAG--TTCGAGTC
1 GAGTTTTA-ATATTATTTTAGAGTTTGAG--GTTTTGAGTTTTCGAGTC
* *
73876 GAGCTTTAATATTATCTTTCGAGTTTGAGGTTTGTGAGTTTTCGAGTC
1 GAGTTTTAATATTAT-TTTAGAGTTTGAGGTTT-TGAGTTTTCGAGTC
73924 GAGTTT
1 GAGTTT
73930 ACATTTAAAG
Statistics
Matches: 74, Mismatches: 8, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
41 12 0.16
42 15 0.20
43 3 0.04
44 4 0.05
45 3 0.04
46 4 0.05
47 15 0.20
48 18 0.24
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.48
Consensus pattern (46 bp):
GAGTTTTAATATTATTTTAGAGTTTGAGGTTTTGAGTTTTCGAGTC
Found at i:73884 original size:89 final size:88
Alignment explanation
Indices: 73771--73942 Score: 256
Period size: 89 Copynumber: 1.9 Consensus size: 88
73761 GAGTTTAAAT
* * * * * *
73771 TTTTTGAGTTTAAGTTGAGTTTTAATATTATTTTTTGAGTTTGAGGTTT-TCGAGTTTTCGAGTT
1 TTTTTGAGTTCAAGTCGAGCTTTAATATTATCTTTCGAGTTTGAGGTTTGT-GAGTTTTCGAGTC
73835 GAGTTTACATTTAAGAGTTTAAGCC
65 GAGTTTACATTTAA-AGTTTAAGCC
*
73860 TTTTTGAGTTCGAGTCGAGCTTTAATATTATCTTTCGAGTTTGAGGTTTGTGAGTTTTCGAGTCG
1 TTTTTGAGTTCAAGTCGAGCTTTAATATTATCTTTCGAGTTTGAGGTTTGTGAGTTTTCGAGTCG
73925 AGTTTACATTTAAAGTTT
66 AGTTTACATTTAAAGTTT
73943 TTGAGTTCGA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
88 5 0.07
89 69 0.92
90 1 0.01
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.49
Consensus pattern (88 bp):
TTTTTGAGTTCAAGTCGAGCTTTAATATTATCTTTCGAGTTTGAGGTTTGTGAGTTTTCGAGTCG
AGTTTACATTTAAAGTTTAAGCC
Found at i:74953 original size:25 final size:26
Alignment explanation
Indices: 74919--74976 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
74909 CCATCAATCC
74919 AAGGGGAGAGGAA-CTGGTGTAGCCT
1 AAGGGGAGAGGAACCTGGTGTAGCCT
74944 AAGGGGAGAGGAACCTGGTGTAGCCT
1 AAGGGGAGAGGAACCTGGTGTAGCCT
*
74970 CAGGGGA
1 AAGGGGA
74977 ACATCGACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.28, C:0.14, G:0.45, T:0.14
Consensus pattern (26 bp):
AAGGGGAGAGGAACCTGGTGTAGCCT
Found at i:76031 original size:2 final size:2
Alignment explanation
Indices: 76024--76049 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
76014 CCTCATTACC
76024 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
76050 CTTATAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:85236 original size:21 final size:21
Alignment explanation
Indices: 85198--85237 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
85188 GTTTCCAAAC
*
85198 ATTAAACAGACATATTCACGA
1 ATTAAACAAACATATTCACGA
* *
85219 ATTAAACAAATATGTTCAC
1 ATTAAACAAACATATTCAC
85238 TAACGTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.28
Consensus pattern (21 bp):
ATTAAACAAACATATTCACGA
Found at i:85355 original size:26 final size:25
Alignment explanation
Indices: 85313--85361 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
85303 TTAGAAAAAA
*
85313 AAAAGATAAACAAACACGAACATTC
1 AAAAGATAAACAAACACAAACATTC
85338 AAAA-ATAAACAACGACACAAACAT
1 AAAAGATAAACAA--ACACAAACAT
85362 AACTTTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 4 0.19
26 9 0.43
ACGTcount: A:0.63, C:0.20, G:0.06, T:0.10
Consensus pattern (25 bp):
AAAAGATAAACAAACACAAACATTC
Done.